From 68ea7be4ce107685995da17ccda7fcee8220ad71 Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Tue, 31 Mar 2020 23:18:37 +0200
Subject: [PATCH 01/22] upgrade rpy2 version

---
 build/pkgs/rpy2/checksums.ini       | 6 +++---
 build/pkgs/rpy2/package-version.txt | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/build/pkgs/rpy2/checksums.ini b/build/pkgs/rpy2/checksums.ini
index c6670edbb27..808cb371fc0 100644
--- a/build/pkgs/rpy2/checksums.ini
+++ b/build/pkgs/rpy2/checksums.ini
@@ -1,4 +1,4 @@
 tarball=rpy2-VERSION.tar.gz
-sha1=24f7c538a734618dfcf2343304729c0b1e429717
-md5=729946166b43103db7697e69db8c5c45
-cksum=3858682977
+sha1=05ad6e4a8c4912a5bc8b403f1772f5e04d4ec173
+md5=eaa65c233eb2d60678dabe2b58894aa4
+cksum=282685783
diff --git a/build/pkgs/rpy2/package-version.txt b/build/pkgs/rpy2/package-version.txt
index 4b18da28f6e..406ebcbd95f 100644
--- a/build/pkgs/rpy2/package-version.txt
+++ b/build/pkgs/rpy2/package-version.txt
@@ -1 +1 @@
-2.8.2.p1
+3.2.7

From f1cd4e2ef423bccdeac62218a6c5140182a622a9 Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Tue, 31 Mar 2020 23:18:54 +0200
Subject: [PATCH 02/22] remove cygwin.patch (rpy2)

---
 build/pkgs/rpy2/patches/cygwin.patch | 108 ---------------------------
 1 file changed, 108 deletions(-)
 delete mode 100644 build/pkgs/rpy2/patches/cygwin.patch

diff --git a/build/pkgs/rpy2/patches/cygwin.patch b/build/pkgs/rpy2/patches/cygwin.patch
deleted file mode 100644
index d2088e419e1..00000000000
--- a/build/pkgs/rpy2/patches/cygwin.patch
+++ /dev/null
@@ -1,108 +0,0 @@
-diff -ru rpy2-2.7.4.orig/rpy/rinterface/na_values.c rpy2-2.7.4/rpy/rinterface/na_values.c
---- rpy2-2.7.4.orig/rpy/rinterface/na_values.c	2015-09-05 01:15:16.000000000 +0200
-+++ rpy2-2.7.4/rpy/rinterface/na_values.c	2015-12-01 11:46:40.675932500 +0100
-@@ -203,7 +203,7 @@
-         0,                      /*tp_methods*/
-         0,                      /*tp_members*/
-         0,                      /*tp_getset*/
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
- 	NULL,
- #else	
-         &PyLong_Type,           /*tp_base*/
-@@ -401,7 +401,7 @@
-         0, //NAInteger_methods,           /*tp_methods*/
-         0,                      /*tp_members*/
-         0,                      /*tp_getset*/
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
- 	NULL,
- #else
-         &PyLong_Type,             /*tp_base*/
-@@ -587,7 +587,7 @@
-         0, //NAInteger_methods,           /*tp_methods*/
-         0,                      /*tp_members*/
-         0,                      /*tp_getset*/
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
- 	NULL,
- #else
-         &PyFloat_Type,             /*tp_base*/
-@@ -689,7 +689,7 @@
-         0, //NAInteger_methods,           /*tp_methods*/
-         0,                      /*tp_members*/
-         0,                      /*tp_getset*/
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
- 	NULL,
- #elif (PY_VERSION_HEX < 0x03010000)
-         &PyString_Type,             /*tp_base*/
-@@ -856,7 +856,7 @@
-         0, //NAInteger_methods,           /*tp_methods*/
-         0,                      /*tp_members*/
-         0,                      /*tp_getset*/
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
- 	NULL,
- #else
-         &PyComplex_Type,             /*tp_base*/
-diff -ru rpy2-2.7.4.orig/rpy/rinterface/_rinterface.c rpy2-2.7.4/rpy/rinterface/_rinterface.c
---- rpy2-2.7.4.orig/rpy/rinterface/_rinterface.c	2015-09-12 23:23:55.000000000 +0200
-+++ rpy2-2.7.4/rpy/rinterface/_rinterface.c	2015-12-01 11:45:53.163820335 +0100
-@@ -1162,7 +1162,7 @@
-              "and R_runHandlers (on other platforms).");
- 
- 
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
- void win32CallBack()
- {
-    /* called during i/o, eval, graphics in ProcessEvents */
-@@ -3749,7 +3749,7 @@
-   }
- 
-   /* NA types */
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
-   NAInteger_Type.tp_base=&PyLong_Type;
- #endif
-   if (PyType_Ready(&NAInteger_Type) < 0) {
-@@ -3759,7 +3759,7 @@
-     return NULL;
- #endif
-   }
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
-   NALogical_Type.tp_base=&PyLong_Type;
- #endif
-   if (PyType_Ready(&NALogical_Type) < 0) {
-@@ -3769,7 +3769,7 @@
-     return NULL;
- #endif
-   }
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
-   NAReal_Type.tp_base=&PyFloat_Type;
- #endif
-   if (PyType_Ready(&NAReal_Type) < 0) {
-@@ -3779,7 +3779,7 @@
-     return NULL;
- #endif
-   }
--#if defined(Win32) || defined(Win64)
-+#if defined(Win32) || defined(Win64) || defined(__CYGWIN__)
-   NAComplex_Type.tp_base=&PyComplex_Type;
- #endif
-   if (PyType_Ready(&NAComplex_Type) < 0) {
-diff -ru rpy2-2.7.4.orig/setup rpy2-2.7.4/setup.py
---- rpy2-2.7.4.orig/setup.py       2016-01-15 01:45:48.447894400 -0800
-+++ rpy2-2.7.4/setup.py    2016-01-15 01:48:55.222874000 -0800
-@@ -160,7 +160,7 @@
-     extra_link_args = []
-     extra_compile_args = []
-     include_dirs = []
--    libraries = []
-+    libraries = ['readline']
-     library_dirs = []
-
-     #FIXME: crude way (will break in many cases)

From 68f6f928b4042228cbd1f2bb8c2b102a79eec992 Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Tue, 31 Mar 2020 23:19:07 +0200
Subject: [PATCH 03/22] add setup.patch (rpy2)

---
 build/pkgs/rpy2/patches/setup.patch | 16 ++++++++++++++++
 1 file changed, 16 insertions(+)
 create mode 100644 build/pkgs/rpy2/patches/setup.patch

diff --git a/build/pkgs/rpy2/patches/setup.patch b/build/pkgs/rpy2/patches/setup.patch
new file mode 100644
index 00000000000..d9a03da11c4
--- /dev/null
+++ b/build/pkgs/rpy2/patches/setup.patch
@@ -0,0 +1,16 @@
+diff --git a/setup.py b/setup.py
+index a9f96f8..e82ca80 100755
+--- a/setup.py
++++ b/setup.py
+@@ -182,11 +182,3 @@ if __name__ == '__main__':
+         package_data={'rpy2': ['rinterface_lib/R_API.h',
+                                'rinterface_lib/R_API_eventloop.h']}
+     )
+-
+-    print('---')
+-    if 'rpy2/_rinterface_cffi_build.py:ffibuilder_abi' in cffi_modules:
+-        print('ABI mode interface built and installed')
+-    if 'rpy2/_rinterface_cffi_build.py:ffibuilder_api' in cffi_modules:
+-        print('API mode interface built and installed')
+-    else:
+-        print('API mode interface not build because: %s' % c_extension_status)

From b550f43cefe88466e080ff4fc72bf8cd5c22f8bb Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Tue, 31 Mar 2020 23:48:00 +0200
Subject: [PATCH 04/22] add upstream_url field to rpy2 checksums.ini

---
 build/pkgs/rpy2/checksums.ini | 1 +
 1 file changed, 1 insertion(+)

diff --git a/build/pkgs/rpy2/checksums.ini b/build/pkgs/rpy2/checksums.ini
index 808cb371fc0..9c71a70b04f 100644
--- a/build/pkgs/rpy2/checksums.ini
+++ b/build/pkgs/rpy2/checksums.ini
@@ -2,3 +2,4 @@ tarball=rpy2-VERSION.tar.gz
 sha1=05ad6e4a8c4912a5bc8b403f1772f5e04d4ec173
 md5=eaa65c233eb2d60678dabe2b58894aa4
 cksum=282685783
+upstream_url=https://files.pythonhosted.org/packages/39/c0/61120f9dae06b4887426d229b68a7a5f0ca1f9cb3986319bb9484819a28d/rpy2-3.2.7.tar.gz

From 2cd2191f620f82cddaa047d8db3a4f81433d1be9 Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Tue, 31 Mar 2020 23:58:14 +0200
Subject: [PATCH 05/22] let rpy2 not depend on pytest

---
 build/pkgs/rpy2/patches/setup.patch | 27 +++++++++++++++++++++++++--
 1 file changed, 25 insertions(+), 2 deletions(-)

diff --git a/build/pkgs/rpy2/patches/setup.patch b/build/pkgs/rpy2/patches/setup.patch
index d9a03da11c4..72346553571 100644
--- a/build/pkgs/rpy2/patches/setup.patch
+++ b/build/pkgs/rpy2/patches/setup.patch
@@ -1,8 +1,31 @@
 diff --git a/setup.py b/setup.py
-index a9f96f8..e82ca80 100755
+index a9f96f8..7ba69a1 100755
 --- a/setup.py
 +++ b/setup.py
-@@ -182,11 +182,3 @@ if __name__ == '__main__':
+@@ -142,7 +142,7 @@ ipython.
+ if __name__ == '__main__':
+     pack_dir = {PACKAGE_NAME: os.path.join(package_prefix, 'rpy2')}
+         
+-    requires = ['pytest', 'jinja2', 'pytz', 'simplegeneric', 'tzlocal']
++    requires = ['jinja2', 'pytz', 'simplegeneric', 'tzlocal']
+     
+     setup(
+         name=PACKAGE_NAME,
+@@ -161,12 +161,7 @@ if __name__ == '__main__':
+         packages=([PACKAGE_NAME] +
+                   ['{pack_name}.{x}'.format(pack_name=PACKAGE_NAME, x=x)
+                    for x in ('rlike', 'rinterface_lib', 'robjects',
+-                             'robjects.lib', 'interactive', 'ipython',
+-                             'tests',
+-                             'tests.rinterface', 'tests.rlike',
+-                             'tests.robjects',
+-                             'tests.ipython',
+-                             'tests.robjects.lib')]
++                             'robjects.lib', 'interactive', 'ipython')]
+         ),
+         classifiers = ['Programming Language :: Python',
+                        'Programming Language :: Python :: 3',
+@@ -182,11 +177,3 @@ if __name__ == '__main__':
          package_data={'rpy2': ['rinterface_lib/R_API.h',
                                 'rinterface_lib/R_API_eventloop.h']}
      )

From b76ee25d67fccc77e1f4ba7fb0f4589c022bca4f Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Wed, 1 Apr 2020 00:13:55 +0200
Subject: [PATCH 06/22] cffi package (rpy2 dependency)

---
 build/pkgs/cffi/SPKG.txt            | 15 +++++++++++++++
 build/pkgs/cffi/checksums.ini       |  5 +++++
 build/pkgs/cffi/package-version.txt |  1 +
 build/pkgs/cffi/spkg-install.in     |  1 +
 build/pkgs/cffi/type                |  1 +
 5 files changed, 23 insertions(+)
 create mode 100644 build/pkgs/cffi/SPKG.txt
 create mode 100644 build/pkgs/cffi/checksums.ini
 create mode 100644 build/pkgs/cffi/package-version.txt
 create mode 100644 build/pkgs/cffi/spkg-install.in
 create mode 100644 build/pkgs/cffi/type

diff --git a/build/pkgs/cffi/SPKG.txt b/build/pkgs/cffi/SPKG.txt
new file mode 100644
index 00000000000..075e8abf25b
--- /dev/null
+++ b/build/pkgs/cffi/SPKG.txt
@@ -0,0 +1,15 @@
+= cffi =
+
+== Description ==
+
+development website: https://foss.heptapod.net/pypy/cffi
+documentation website: https://cffi.readthedocs.io/en/latest/
+PyPI page: https://pypi.org/project/cffi/
+
+== License ==
+
+ * MIT
+
+== Upstream Contact ==
+
+ * https://foss.heptapod.net/pypy/cffi
diff --git a/build/pkgs/cffi/checksums.ini b/build/pkgs/cffi/checksums.ini
new file mode 100644
index 00000000000..710656a87a7
--- /dev/null
+++ b/build/pkgs/cffi/checksums.ini
@@ -0,0 +1,5 @@
+tarball=cffi-VERSION.tar.gz
+sha1=2a8f05a7d51d77ef1e641cb359a54e4d8fa019cb
+md5=74845f8d2b7b583dd9a3574f402edf39
+cksum=1594930691
+upstream_url=https://files.pythonhosted.org/packages/05/54/3324b0c46340c31b909fcec598696aaec7ddc8c18a63f2db352562d3354c/cffi-1.14.0.tar.gz
diff --git a/build/pkgs/cffi/package-version.txt b/build/pkgs/cffi/package-version.txt
new file mode 100644
index 00000000000..850e742404b
--- /dev/null
+++ b/build/pkgs/cffi/package-version.txt
@@ -0,0 +1 @@
+1.14.0
diff --git a/build/pkgs/cffi/spkg-install.in b/build/pkgs/cffi/spkg-install.in
new file mode 100644
index 00000000000..deba1bb42bb
--- /dev/null
+++ b/build/pkgs/cffi/spkg-install.in
@@ -0,0 +1 @@
+cd src && sdh_pip_install .
diff --git a/build/pkgs/cffi/type b/build/pkgs/cffi/type
new file mode 100644
index 00000000000..a6a7b9cd726
--- /dev/null
+++ b/build/pkgs/cffi/type
@@ -0,0 +1 @@
+standard

From 84ded30cafa163fd19da294d546dd24ff6550e46 Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Wed, 1 Apr 2020 00:14:10 +0200
Subject: [PATCH 07/22] pycparser (rpy2 dependency)

---
 build/pkgs/pycparser/SPKG.txt            | 15 +++++++++++++++
 build/pkgs/pycparser/checksums.ini       |  5 +++++
 build/pkgs/pycparser/package-version.txt |  1 +
 build/pkgs/pycparser/spkg-install.in     |  1 +
 build/pkgs/pycparser/type                |  1 +
 5 files changed, 23 insertions(+)
 create mode 100644 build/pkgs/pycparser/SPKG.txt
 create mode 100644 build/pkgs/pycparser/checksums.ini
 create mode 100644 build/pkgs/pycparser/package-version.txt
 create mode 100644 build/pkgs/pycparser/spkg-install.in
 create mode 100644 build/pkgs/pycparser/type

diff --git a/build/pkgs/pycparser/SPKG.txt b/build/pkgs/pycparser/SPKG.txt
new file mode 100644
index 00000000000..56334914f0d
--- /dev/null
+++ b/build/pkgs/pycparser/SPKG.txt
@@ -0,0 +1,15 @@
+= pycparser =
+
+== Description ==
+
+development website: https://github.com/eliben/pycparser
+PyPI page: https://pypi.org/project/pycparser/
+
+== License ==
+
+ * BSD
+
+== Upstream Contact ==
+
+ * https://github.com/eliben/pycparser
+
diff --git a/build/pkgs/pycparser/checksums.ini b/build/pkgs/pycparser/checksums.ini
new file mode 100644
index 00000000000..9ad2ce58fb5
--- /dev/null
+++ b/build/pkgs/pycparser/checksums.ini
@@ -0,0 +1,5 @@
+tarball=pycparser-VERSION.tar.gz
+sha1=0ae93d89b69fab48af3a407a2f8663bcea270c3d
+md5=b8f88de737db8c346ee8d31c07c7a25a
+cksum=3289554032
+upstream_url=https://files.pythonhosted.org/packages/0f/86/e19659527668d70be91d0369aeaa055b4eb396b0f387a4f92293a20035bd/pycparser-2.20.tar.gz
diff --git a/build/pkgs/pycparser/package-version.txt b/build/pkgs/pycparser/package-version.txt
new file mode 100644
index 00000000000..a4b5a6f4a49
--- /dev/null
+++ b/build/pkgs/pycparser/package-version.txt
@@ -0,0 +1 @@
+2.20
diff --git a/build/pkgs/pycparser/spkg-install.in b/build/pkgs/pycparser/spkg-install.in
new file mode 100644
index 00000000000..deba1bb42bb
--- /dev/null
+++ b/build/pkgs/pycparser/spkg-install.in
@@ -0,0 +1 @@
+cd src && sdh_pip_install .
diff --git a/build/pkgs/pycparser/type b/build/pkgs/pycparser/type
new file mode 100644
index 00000000000..a6a7b9cd726
--- /dev/null
+++ b/build/pkgs/pycparser/type
@@ -0,0 +1 @@
+standard

From 2e0fe7351b0151e94fca927ddb9e6c15913b2aad Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Wed, 1 Apr 2020 00:14:57 +0200
Subject: [PATCH 08/22] update rpy2 dependencies

---
 build/pkgs/rpy2/dependencies | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/pkgs/rpy2/dependencies b/build/pkgs/rpy2/dependencies
index c939931f297..3fbebabc078 100644
--- a/build/pkgs/rpy2/dependencies
+++ b/build/pkgs/rpy2/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) r six singledispatch | $(PYTHON_TOOLCHAIN)
+$(PYTHON) r cffi | $(PYTHON_TOOLCHAIN) pycparser
 
 ----------
 All lines of this file are ignored except the first.

From 81f580eff5007a666dc712e5219d47f5933e1573 Mon Sep 17 00:00:00 2001
From: Vincent Delecroix <20100.delecroix@gmail.com>
Date: Sun, 19 Apr 2020 23:26:25 +0200
Subject: [PATCH 09/22] still install tests along rpy2

---
 build/pkgs/rpy2/patches/setup.patch | 14 --------------
 1 file changed, 14 deletions(-)

diff --git a/build/pkgs/rpy2/patches/setup.patch b/build/pkgs/rpy2/patches/setup.patch
index 72346553571..3e6f81c2db4 100644
--- a/build/pkgs/rpy2/patches/setup.patch
+++ b/build/pkgs/rpy2/patches/setup.patch
@@ -11,20 +11,6 @@ index a9f96f8..7ba69a1 100755
      
      setup(
          name=PACKAGE_NAME,
-@@ -161,12 +161,7 @@ if __name__ == '__main__':
-         packages=([PACKAGE_NAME] +
-                   ['{pack_name}.{x}'.format(pack_name=PACKAGE_NAME, x=x)
-                    for x in ('rlike', 'rinterface_lib', 'robjects',
--                             'robjects.lib', 'interactive', 'ipython',
--                             'tests',
--                             'tests.rinterface', 'tests.rlike',
--                             'tests.robjects',
--                             'tests.ipython',
--                             'tests.robjects.lib')]
-+                             'robjects.lib', 'interactive', 'ipython')]
-         ),
-         classifiers = ['Programming Language :: Python',
-                        'Programming Language :: Python :: 3',
 @@ -182,11 +177,3 @@ if __name__ == '__main__':
          package_data={'rpy2': ['rinterface_lib/R_API.h',
                                 'rinterface_lib/R_API_eventloop.h']}

From d4c16728171baa763dcb653f83aa485fdbeedefa Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 3 Jul 2020 12:02:59 -0700
Subject: [PATCH 10/22] build/pkgs: Upgrade rpy2 to 3.3.4, use patterns for
 upstream_urls of dependencies

---
 build/pkgs/cffi/checksums.ini       | 2 +-
 build/pkgs/pycparser/checksums.ini  | 2 +-
 build/pkgs/rpy2/checksums.ini       | 8 ++++----
 build/pkgs/rpy2/package-version.txt | 2 +-
 4 files changed, 7 insertions(+), 7 deletions(-)

diff --git a/build/pkgs/cffi/checksums.ini b/build/pkgs/cffi/checksums.ini
index 710656a87a7..88dd9628d4c 100644
--- a/build/pkgs/cffi/checksums.ini
+++ b/build/pkgs/cffi/checksums.ini
@@ -2,4 +2,4 @@ tarball=cffi-VERSION.tar.gz
 sha1=2a8f05a7d51d77ef1e641cb359a54e4d8fa019cb
 md5=74845f8d2b7b583dd9a3574f402edf39
 cksum=1594930691
-upstream_url=https://files.pythonhosted.org/packages/05/54/3324b0c46340c31b909fcec598696aaec7ddc8c18a63f2db352562d3354c/cffi-1.14.0.tar.gz
+upstream_url=https://pypi.io/packages/source/c/cffi/cffi-VERSION.tar.gz
diff --git a/build/pkgs/pycparser/checksums.ini b/build/pkgs/pycparser/checksums.ini
index 9ad2ce58fb5..885d94acf9d 100644
--- a/build/pkgs/pycparser/checksums.ini
+++ b/build/pkgs/pycparser/checksums.ini
@@ -2,4 +2,4 @@ tarball=pycparser-VERSION.tar.gz
 sha1=0ae93d89b69fab48af3a407a2f8663bcea270c3d
 md5=b8f88de737db8c346ee8d31c07c7a25a
 cksum=3289554032
-upstream_url=https://files.pythonhosted.org/packages/0f/86/e19659527668d70be91d0369aeaa055b4eb396b0f387a4f92293a20035bd/pycparser-2.20.tar.gz
+upstream_url=https://pypi.io/packages/source/p/pycparser/pycparser-VERSION.tar.gz
diff --git a/build/pkgs/rpy2/checksums.ini b/build/pkgs/rpy2/checksums.ini
index 9c71a70b04f..6cb4be003c2 100644
--- a/build/pkgs/rpy2/checksums.ini
+++ b/build/pkgs/rpy2/checksums.ini
@@ -1,5 +1,5 @@
 tarball=rpy2-VERSION.tar.gz
-sha1=05ad6e4a8c4912a5bc8b403f1772f5e04d4ec173
-md5=eaa65c233eb2d60678dabe2b58894aa4
-cksum=282685783
-upstream_url=https://files.pythonhosted.org/packages/39/c0/61120f9dae06b4887426d229b68a7a5f0ca1f9cb3986319bb9484819a28d/rpy2-3.2.7.tar.gz
+sha1=64762fe2abe3a6469975ff86187396f8339f85e4
+md5=da70a5c4e35e22c469c37444d45257ee
+cksum=2800144752
+upstream_url=https://pypi.io/packages/source/r/rpy2/rpy2-VERSION.tar.gz
diff --git a/build/pkgs/rpy2/package-version.txt b/build/pkgs/rpy2/package-version.txt
index 406ebcbd95f..a0891f563f3 100644
--- a/build/pkgs/rpy2/package-version.txt
+++ b/build/pkgs/rpy2/package-version.txt
@@ -1 +1 @@
-3.2.7
+3.3.4

From 28552a28400afe4afd1ff2e51b64b1a09271e659 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 3 Jul 2020 21:29:16 -0700
Subject: [PATCH 11/22] Update patches

---
 build/pkgs/rpy2/patches/716.patch             | 89 +++++++++++++++++++
 build/pkgs/rpy2/patches/setup-no-pytest.patch | 13 +++
 build/pkgs/rpy2/patches/setup.patch           | 25 ------
 3 files changed, 102 insertions(+), 25 deletions(-)
 create mode 100644 build/pkgs/rpy2/patches/716.patch
 create mode 100644 build/pkgs/rpy2/patches/setup-no-pytest.patch
 delete mode 100644 build/pkgs/rpy2/patches/setup.patch

diff --git a/build/pkgs/rpy2/patches/716.patch b/build/pkgs/rpy2/patches/716.patch
new file mode 100644
index 00000000000..8446b281633
--- /dev/null
+++ b/build/pkgs/rpy2/patches/716.patch
@@ -0,0 +1,89 @@
+From 87d0f82e2f4be94893881913018ca9085c0ff8e5 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Fri, 3 Jul 2020 12:47:41 -0700
+Subject: [PATCH] setup.py: Print CFFI configuration messages only on build
+
+---
+ setup.py | 44 ++++++++++++++++++++++++++------------------
+ 1 file changed, 26 insertions(+), 18 deletions(-)
+
+diff --git a/setup.py b/setup.py
+index e4337838..7fead893 100755
+--- a/setup.py
++++ b/setup.py
+@@ -21,6 +21,7 @@
+ from rpy2 import situation
+ 
+ from setuptools import setup
++from distutils.command.build import build as du_build
+ 
+ PACKAGE_NAME = 'rpy2'
+ pack_version = __import__('rpy2').__version__
+@@ -111,7 +112,6 @@ def get_r_c_extension_status():
+ 
+ 
+ cffi_mode = situation.get_cffi_mode()
+-print('cffi mode: %s' % cffi_mode)
+ c_extension_status = get_r_c_extension_status()
+ if cffi_mode == situation.CFFI_MODE.ABI:
+     cffi_modules = ['rpy2/_rinterface_cffi_build.py:ffibuilder_abi']
+@@ -135,6 +135,30 @@ def get_r_c_extension_status():
+     # This should never happen.
+     raise ValueError('Invalid value for cffi_mode')
+ 
++class build(du_build):
++
++    def run(self):
++        print('cffi mode: %s' % cffi_mode)
++
++        du_build.run(self)
++
++        print('---')
++        print(cffi_mode)
++        if cffi_mode in (situation.CFFI_MODE.ABI,
++                         situation.CFFI_MODE.BOTH,
++                         situation.CFFI_MODE.ANY):
++            print('ABI mode interface built.')
++        if cffi_mode in (situation.CFFI_MODE.API,
++                         situation.CFFI_MODE.BOTH):
++            print('API mode interface built.')
++        if cffi_mode == situation.CFFI_MODE.ANY:
++            if c_extension_status == COMPILATION_STATUS.OK:
++                print('API mode interface built.')
++            else:
++                print('API mode interface not built because: %s' % c_extension_status)
++        print('To change the API/ABI build mode, set or modify the environment '
++              'variable RPY2_CFFI_MODE.')
++
+ LONG_DESCRIPTION = """
+ Python interface to the R language.
+ 
+@@ -168,6 +192,7 @@ def get_r_c_extension_status():
+         install_requires=requires + ['cffi>=1.10.0'],
+         setup_requires=['cffi>=1.10.0'],
+         cffi_modules=cffi_modules,
++        cmdclass = dict(build=build),
+         package_dir=pack_dir,
+         packages=([PACKAGE_NAME] +
+                   ['{pack_name}.{x}'.format(pack_name=PACKAGE_NAME, x=x)
+@@ -193,20 +218,3 @@ def get_r_c_extension_status():
+         package_data={'rpy2': ['rinterface_lib/R_API.h',
+                                'rinterface_lib/R_API_eventloop.h']}
+     )
+-
+-    print('---')
+-    print(cffi_mode)
+-    if cffi_mode in (situation.CFFI_MODE.ABI,
+-                     situation.CFFI_MODE.BOTH,
+-                     situation.CFFI_MODE.ANY):
+-        print('ABI mode interface built and installed.')
+-    if cffi_mode in (situation.CFFI_MODE.API,
+-                     situation.CFFI_MODE.BOTH):
+-        print('API mode interface built and installed.')
+-    if cffi_mode == situation.CFFI_MODE.ANY:
+-        if c_extension_status == COMPILATION_STATUS.OK:
+-            print('API mode interface built and installed.')
+-        else:
+-            print('API mode interface not build because: %s' % c_extension_status)
+-    print('To change the API/ABI build mode, set or modify the environment '
+-          'variable RPY2_CFFI_MODE.')
diff --git a/build/pkgs/rpy2/patches/setup-no-pytest.patch b/build/pkgs/rpy2/patches/setup-no-pytest.patch
new file mode 100644
index 00000000000..91cb5127572
--- /dev/null
+++ b/build/pkgs/rpy2/patches/setup-no-pytest.patch
@@ -0,0 +1,13 @@
+diff --git a/setup.py b/setup.py
+index a9f96f8..7ba69a1 100755
+--- a/setup.py
++++ b/setup.py
+@@ -142,7 +142,7 @@ ipython.
+ if __name__ == '__main__':
+     pack_dir = {PACKAGE_NAME: os.path.join(package_prefix, 'rpy2')}
+         
+-    requires = ['pytest', 'jinja2', 'pytz', 'tzlocal']
++    requires = ['jinja2', 'pytz', 'tzlocal']
+     
+     setup(
+         name=PACKAGE_NAME,
diff --git a/build/pkgs/rpy2/patches/setup.patch b/build/pkgs/rpy2/patches/setup.patch
deleted file mode 100644
index 3e6f81c2db4..00000000000
--- a/build/pkgs/rpy2/patches/setup.patch
+++ /dev/null
@@ -1,25 +0,0 @@
-diff --git a/setup.py b/setup.py
-index a9f96f8..7ba69a1 100755
---- a/setup.py
-+++ b/setup.py
-@@ -142,7 +142,7 @@ ipython.
- if __name__ == '__main__':
-     pack_dir = {PACKAGE_NAME: os.path.join(package_prefix, 'rpy2')}
-         
--    requires = ['pytest', 'jinja2', 'pytz', 'simplegeneric', 'tzlocal']
-+    requires = ['jinja2', 'pytz', 'simplegeneric', 'tzlocal']
-     
-     setup(
-         name=PACKAGE_NAME,
-@@ -182,11 +177,3 @@ if __name__ == '__main__':
-         package_data={'rpy2': ['rinterface_lib/R_API.h',
-                                'rinterface_lib/R_API_eventloop.h']}
-     )
--
--    print('---')
--    if 'rpy2/_rinterface_cffi_build.py:ffibuilder_abi' in cffi_modules:
--        print('ABI mode interface built and installed')
--    if 'rpy2/_rinterface_cffi_build.py:ffibuilder_api' in cffi_modules:
--        print('API mode interface built and installed')
--    else:
--        print('API mode interface not build because: %s' % c_extension_status)

From 20133ada14046474d5c0a5b563580e6949caeaba Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 3 Jul 2020 21:34:13 -0700
Subject: [PATCH 12/22] build/pkgs/rpy2: Add spkg-check.in, add conditional dep
 on pytest, simplify spkg-install.in

---
 build/pkgs/rpy2/dependencies    | 2 +-
 build/pkgs/rpy2/spkg-check.in   | 1 +
 build/pkgs/rpy2/spkg-install.in | 6 ------
 3 files changed, 2 insertions(+), 7 deletions(-)
 create mode 100644 build/pkgs/rpy2/spkg-check.in

diff --git a/build/pkgs/rpy2/dependencies b/build/pkgs/rpy2/dependencies
index 3fbebabc078..1da6d526a51 100644
--- a/build/pkgs/rpy2/dependencies
+++ b/build/pkgs/rpy2/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) r cffi | $(PYTHON_TOOLCHAIN) pycparser
+$(PYTHON) r cffi | $(PYTHON_TOOLCHAIN) pycparser $(and $(filter-out no,$(SAGE_CHECK)), pytest)
 
 ----------
 All lines of this file are ignored except the first.
diff --git a/build/pkgs/rpy2/spkg-check.in b/build/pkgs/rpy2/spkg-check.in
new file mode 100644
index 00000000000..e079f8a6038
--- /dev/null
+++ b/build/pkgs/rpy2/spkg-check.in
@@ -0,0 +1 @@
+pytest
diff --git a/build/pkgs/rpy2/spkg-install.in b/build/pkgs/rpy2/spkg-install.in
index 105eb0153d0..3098724e3a4 100644
--- a/build/pkgs/rpy2/spkg-install.in
+++ b/build/pkgs/rpy2/spkg-install.in
@@ -1,9 +1,3 @@
-if [ -z "$SAGE_LOCAL" ]; then
-    echo >&2 "SAGE_LOCAL undefined ... exiting"
-    echo >&2 "Maybe run 'sage --sh'?"
-    exit 1
-fi
-
 set -e
 
 cd src

From c02362ea4e827885fc95a356e77ff31d7c1355b5 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 3 Jul 2020 21:41:11 -0700
Subject: [PATCH 13/22] build/pkgs/tzlocal: New (pip package)

---
 build/pkgs/tzlocal/requirements.txt | 1 +
 build/pkgs/tzlocal/type             | 1 +
 2 files changed, 2 insertions(+)
 create mode 100644 build/pkgs/tzlocal/requirements.txt
 create mode 100644 build/pkgs/tzlocal/type

diff --git a/build/pkgs/tzlocal/requirements.txt b/build/pkgs/tzlocal/requirements.txt
new file mode 100644
index 00000000000..cd5e9b12a4b
--- /dev/null
+++ b/build/pkgs/tzlocal/requirements.txt
@@ -0,0 +1 @@
+tzlocal
diff --git a/build/pkgs/tzlocal/type b/build/pkgs/tzlocal/type
new file mode 100644
index 00000000000..134d9bc32d5
--- /dev/null
+++ b/build/pkgs/tzlocal/type
@@ -0,0 +1 @@
+optional

From d33797fe7e8f7a069a39eb446419592916fc90a9 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 3 Jul 2020 21:41:34 -0700
Subject: [PATCH 14/22] build/pkgs/rpy2/dependencies: Add conditional dep on
 tzlocal, numpy

---
 build/pkgs/rpy2/dependencies | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/pkgs/rpy2/dependencies b/build/pkgs/rpy2/dependencies
index 1da6d526a51..7f2d42901ef 100644
--- a/build/pkgs/rpy2/dependencies
+++ b/build/pkgs/rpy2/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) r cffi | $(PYTHON_TOOLCHAIN) pycparser $(and $(filter-out no,$(SAGE_CHECK)), pytest)
+$(PYTHON) r cffi | $(PYTHON_TOOLCHAIN) pycparser $(and $(filter-out no,$(SAGE_CHECK)), pytest tzlocal numpy)
 
 ----------
 All lines of this file are ignored except the first.

From b66e9df749993b975920a440f870bc3f6df19884 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Sat, 4 Jul 2020 08:46:22 -0700
Subject: [PATCH 15/22] build/pkgs/{cffi,pycparser}/dependencies: New

---
 build/pkgs/cffi/dependencies      | 5 +++++
 build/pkgs/pycparser/dependencies | 5 +++++
 2 files changed, 10 insertions(+)
 create mode 100644 build/pkgs/cffi/dependencies
 create mode 100644 build/pkgs/pycparser/dependencies

diff --git a/build/pkgs/cffi/dependencies b/build/pkgs/cffi/dependencies
new file mode 100644
index 00000000000..15df0c4d6d8
--- /dev/null
+++ b/build/pkgs/cffi/dependencies
@@ -0,0 +1,5 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/pycparser/dependencies b/build/pkgs/pycparser/dependencies
new file mode 100644
index 00000000000..15df0c4d6d8
--- /dev/null
+++ b/build/pkgs/pycparser/dependencies
@@ -0,0 +1,5 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.

From 3b14bf51517e2c8c77a49dcc286fe6dfaf38dc48 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Sat, 11 Jul 2020 22:10:53 -0700
Subject: [PATCH 16/22] build/pkgs/rpy2/dependencies: Conditionalize on
 SAGE_CHECK_rpy2

---
 build/pkgs/rpy2/dependencies | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/pkgs/rpy2/dependencies b/build/pkgs/rpy2/dependencies
index 7f2d42901ef..4e37a7ddf02 100644
--- a/build/pkgs/rpy2/dependencies
+++ b/build/pkgs/rpy2/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) r cffi | $(PYTHON_TOOLCHAIN) pycparser $(and $(filter-out no,$(SAGE_CHECK)), pytest tzlocal numpy)
+$(PYTHON) r cffi | $(PYTHON_TOOLCHAIN) pycparser $(and $(filter-out no,$(SAGE_CHECK_rpy2)), pytest tzlocal numpy)
 
 ----------
 All lines of this file are ignored except the first.

From 5f93e7f059fcbfa3eecf1dd22112fb647498a506 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Thu, 16 Jul 2020 10:21:43 -0700
Subject: [PATCH 17/22] build/pkgs/pytz: Update to 2020.1

---
 build/pkgs/pytz/checksums.ini       | 9 +++++----
 build/pkgs/pytz/package-version.txt | 2 +-
 2 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/build/pkgs/pytz/checksums.ini b/build/pkgs/pytz/checksums.ini
index 08b15bb59c5..d4db734e428 100644
--- a/build/pkgs/pytz/checksums.ini
+++ b/build/pkgs/pytz/checksums.ini
@@ -1,4 +1,5 @@
-tarball=pytz-VERSION.tar.bz2
-sha1=8a01d7f19c8b8b189827e026b76c51be4b537b89
-md5=4b91594c440aa20c76ac92043efa75e1
-cksum=591864951
+tarball=pytz-VERSION.tar.gz
+sha1=60f6db35e92688c4701c16bd3d2b9cbfac1fd604
+md5=0349106ac02f2bfe565dd6d5594e3a15
+cksum=1599443821
+upstream_url=https://pypi.io/packages/source/p/pytz/pytz-VERSION.tar.gz
diff --git a/build/pkgs/pytz/package-version.txt b/build/pkgs/pytz/package-version.txt
index b3d91a9d2f9..b0a4aa2fe24 100644
--- a/build/pkgs/pytz/package-version.txt
+++ b/build/pkgs/pytz/package-version.txt
@@ -1 +1 @@
-2018.7
+2020.1

From 091ed905e020537a18ff6f7c1251c87253537a0d Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Thu, 16 Jul 2020 10:26:55 -0700
Subject: [PATCH 18/22] build/pkgs/tzlocal: Make it a normal, standard package
 (new dep of standard package rpy2)

---
 build/pkgs/tzlocal/SPKG.rst            | 16 ++++++++++++++++
 build/pkgs/tzlocal/checksums.ini       |  5 +++++
 build/pkgs/tzlocal/dependencies        |  5 +++++
 build/pkgs/tzlocal/package-version.txt |  1 +
 build/pkgs/tzlocal/requirements.txt    |  1 -
 build/pkgs/tzlocal/spkg-install.in     |  1 +
 build/pkgs/tzlocal/type                |  2 +-
 7 files changed, 29 insertions(+), 2 deletions(-)
 create mode 100644 build/pkgs/tzlocal/SPKG.rst
 create mode 100644 build/pkgs/tzlocal/checksums.ini
 create mode 100644 build/pkgs/tzlocal/dependencies
 create mode 100644 build/pkgs/tzlocal/package-version.txt
 delete mode 100644 build/pkgs/tzlocal/requirements.txt
 create mode 100644 build/pkgs/tzlocal/spkg-install.in

diff --git a/build/pkgs/tzlocal/SPKG.rst b/build/pkgs/tzlocal/SPKG.rst
new file mode 100644
index 00000000000..ebeba1ad914
--- /dev/null
+++ b/build/pkgs/tzlocal/SPKG.rst
@@ -0,0 +1,16 @@
+pytz
+====
+
+Description
+-----------
+
+World Timezone Definitions for Python
+
+
+Special Update/Build Instructions
+---------------------------------
+
+The upstream tarball was repackaged after sanitizing the file
+permissions with
+
+$ chmod go-w
diff --git a/build/pkgs/tzlocal/checksums.ini b/build/pkgs/tzlocal/checksums.ini
new file mode 100644
index 00000000000..d595a9d3d16
--- /dev/null
+++ b/build/pkgs/tzlocal/checksums.ini
@@ -0,0 +1,5 @@
+tarball=tzlocal-VERSION.tar.gz
+sha1=7d2d590f68849e6b6371210bd808b40ec5619faf
+md5=c0877603ff9de71cd8ca6ee2b50d2ebd
+cksum=950088034
+upstream_url=https://pypi.io/packages/source/t/tzlocal/tzlocal-VERSION.tar.gz
diff --git a/build/pkgs/tzlocal/dependencies b/build/pkgs/tzlocal/dependencies
new file mode 100644
index 00000000000..15df0c4d6d8
--- /dev/null
+++ b/build/pkgs/tzlocal/dependencies
@@ -0,0 +1,5 @@
+$(PYTHON) | $(PYTHON_TOOLCHAIN)
+
+----------
+All lines of this file are ignored except the first.
+It is copied by SAGE_ROOT/build/make/install into SAGE_ROOT/build/make/Makefile.
diff --git a/build/pkgs/tzlocal/package-version.txt b/build/pkgs/tzlocal/package-version.txt
new file mode 100644
index 00000000000..879b416e609
--- /dev/null
+++ b/build/pkgs/tzlocal/package-version.txt
@@ -0,0 +1 @@
+2.1
diff --git a/build/pkgs/tzlocal/requirements.txt b/build/pkgs/tzlocal/requirements.txt
deleted file mode 100644
index cd5e9b12a4b..00000000000
--- a/build/pkgs/tzlocal/requirements.txt
+++ /dev/null
@@ -1 +0,0 @@
-tzlocal
diff --git a/build/pkgs/tzlocal/spkg-install.in b/build/pkgs/tzlocal/spkg-install.in
new file mode 100644
index 00000000000..deba1bb42bb
--- /dev/null
+++ b/build/pkgs/tzlocal/spkg-install.in
@@ -0,0 +1 @@
+cd src && sdh_pip_install .
diff --git a/build/pkgs/tzlocal/type b/build/pkgs/tzlocal/type
index 134d9bc32d5..a6a7b9cd726 100644
--- a/build/pkgs/tzlocal/type
+++ b/build/pkgs/tzlocal/type
@@ -1 +1 @@
-optional
+standard

From b01e92dd86b042c17d2bb17d44354d60bef861ab Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Thu, 16 Jul 2020 10:28:11 -0700
Subject: [PATCH 19/22] build/pkgs/rpy2/dependencies: Add tzlocal pytz as
 normal dependencies

---
 build/pkgs/rpy2/dependencies | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/build/pkgs/rpy2/dependencies b/build/pkgs/rpy2/dependencies
index 4e37a7ddf02..215375ee02d 100644
--- a/build/pkgs/rpy2/dependencies
+++ b/build/pkgs/rpy2/dependencies
@@ -1,4 +1,4 @@
-$(PYTHON) r cffi | $(PYTHON_TOOLCHAIN) pycparser $(and $(filter-out no,$(SAGE_CHECK_rpy2)), pytest tzlocal numpy)
+$(PYTHON) r cffi tzlocal pytz | $(PYTHON_TOOLCHAIN) pycparser $(and $(filter-out no,$(SAGE_CHECK_rpy2)), pytest numpy)
 
 ----------
 All lines of this file are ignored except the first.

From 4ce897074e0570143ec4642a91bf2d846f313635 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Thu, 16 Jul 2020 10:49:41 -0700
Subject: [PATCH 20/22] build/pkgs/rpy2: Update to 3.3.5

---
 build/pkgs/rpy2/checksums.ini       | 6 +++---
 build/pkgs/rpy2/package-version.txt | 2 +-
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/build/pkgs/rpy2/checksums.ini b/build/pkgs/rpy2/checksums.ini
index 6cb4be003c2..9b7f0ea2ec3 100644
--- a/build/pkgs/rpy2/checksums.ini
+++ b/build/pkgs/rpy2/checksums.ini
@@ -1,5 +1,5 @@
 tarball=rpy2-VERSION.tar.gz
-sha1=64762fe2abe3a6469975ff86187396f8339f85e4
-md5=da70a5c4e35e22c469c37444d45257ee
-cksum=2800144752
+sha1=af1c7ffe900233ac5add5195f106299bd72fd575
+md5=8a5db07798763b9c6672b5f80451b944
+cksum=828149660
 upstream_url=https://pypi.io/packages/source/r/rpy2/rpy2-VERSION.tar.gz
diff --git a/build/pkgs/rpy2/package-version.txt b/build/pkgs/rpy2/package-version.txt
index a0891f563f3..fa7adc7ac72 100644
--- a/build/pkgs/rpy2/package-version.txt
+++ b/build/pkgs/rpy2/package-version.txt
@@ -1 +1 @@
-3.3.4
+3.3.5

From 11448a68499ee087ad7cac6e0c979cdf9f01a370 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Fri, 20 Mar 2020 12:24:37 -0400
Subject: [PATCH 21/22] Update R to 3.6.3, add upstream_url

---
 build/pkgs/r/checksums.ini       | 7 ++++---
 build/pkgs/r/package-version.txt | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/build/pkgs/r/checksums.ini b/build/pkgs/r/checksums.ini
index b97750a51de..69a1a7059dc 100644
--- a/build/pkgs/r/checksums.ini
+++ b/build/pkgs/r/checksums.ini
@@ -1,4 +1,5 @@
 tarball=R-VERSION.tar.gz
-sha1=8eda2af51d63877fcc6674274b6801af605173c5
-md5=90d23d138cee26d275da14b58296e521
-cksum=1222866983
+sha1=d2383dabc0d6c70f8a0171a0fb1bfdc31ddb5b52
+md5=506c9576ba33e1262ad5b5624db9d96a
+cksum=2403187565
+upstream_url=https://cran.r-project.org/src/base/R-3/R-VERSION.tar.gz
diff --git a/build/pkgs/r/package-version.txt b/build/pkgs/r/package-version.txt
index e4097539c1a..4a788a01dad 100644
--- a/build/pkgs/r/package-version.txt
+++ b/build/pkgs/r/package-version.txt
@@ -1 +1 @@
-3.6.2.p0
+3.6.3

From 9d667e828a60c0782c60876d8b470d20b035d1c9 Mon Sep 17 00:00:00 2001
From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
Date: Thu, 23 Jul 2020 11:50:33 -0700
Subject: [PATCH 22/22] build/pkgs/r/spkg-install.in: Set rpath

---
 build/pkgs/r/spkg-install.in | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/build/pkgs/r/spkg-install.in b/build/pkgs/r/spkg-install.in
index d77db37688d..905fc2a6150 100644
--- a/build/pkgs/r/spkg-install.in
+++ b/build/pkgs/r/spkg-install.in
@@ -100,6 +100,14 @@ fi
 # See patches/R.sh.patch
 export SAGE_BUILDING_R=yes
 
+R_HOME="$SAGE_LOCAL"/lib/R
+# Set LDFLAGS as it is done in sage-env for $SAGE_LOCAL/lib
+LDFLAGS="-L$R_HOME/lib -Wl,-rpath,$R_HOME/lib $LDFLAGS"
+if [ "$UNAME" = "Linux" ]; then
+    LDFLAGS="-Wl,-rpath-link,$R_HOME/lib $LDFLAGS"
+fi
+export LDFLAGS
+
 config() {
     sdh_configure --enable-R-shlib --with-recommended-packages \
                   --with-readline=yes --with-x=$XSUPPORT \