Merge tag '9.1.beta7' into t/29273/packages/r_packages_in_distros

SageMath version 9.1.beta7, Release Date: 2020-03-08

.gitignore

@@ -97,3 +97,8 @@ gitlab-build-docker.log
 /src/bin/sage-env-config
 /build/bin/sage-build-env-config
 
+#######################
+# tox generated files #
+#######################
+
+/.tox

VERSION.txt

@@ -1 +1 @@
-SageMath version 9.1.beta6, Release Date: 2020-03-01
+SageMath version 9.1.beta7, Release Date: 2020-03-08

build/bin/sage-build-env-config.in

@@ -19,6 +19,9 @@
 #
 ##########################################################################
 
+# The configured CXX without special flags added that enable C++11 support
+export SAGE_CXX_WITHOUT_STD="@SAGE_CXX_WITHOUT_STD@"
+
 # This is usually blank if the system GMP is used, or $SAGE_LOCAL otherwise
 export SAGE_GMP_PREFIX="@SAGE_GMP_PREFIX@"
 export SAGE_GMP_INCLUDE="@SAGE_GMP_INCLUDE@"

build/bin/write-dockerfile.sh

@@ -138,7 +138,6 @@ ADD build ./build
 ADD src/bin/sage-version.sh src/bin/sage-version.sh
 $RUN ./bootstrap
 #:configuring:
-ADD src/ext src/ext
 ADD src/bin src/bin
 ADD src/Makefile.in src/Makefile.in
 ARG EXTRA_CONFIGURE_ARGS=""

build/pkgs/configure/checksums.ini

@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=63dd5a30099d2285ba7d8914dc6a94213e704258
-md5=767a51cc156fec7e49d08cbaefc38d24
-cksum=1354891695
+sha1=7dcc12151cfd28e51461d4fd3495e1dbe40db8f0
+md5=536088bf9fed3f0904958b51bc872c43
+cksum=1081491918

build/pkgs/configure/package-version.txt

@@ -1 +1 @@
-30cb9d11bc3889744a2a27db00041d9cb40df522
+d77360886b95a58e3b7ba146fa464c91a0790876

build/pkgs/dateutil/checksums.ini

@@ -1,4 +1,4 @@
 tarball=python-dateutil-VERSION.tar.gz
-sha1=a53ebfeecc784ea5781ba504ddf7f4ad13738213
-md5=05ffc6d2cc85a7fd93bb245807f715ef
-cksum=1879066915
+sha1=bd26127e57f83a10f656b62c46524c15aeb844dd
+md5=f2a1d4b680b297b367a974664ca3a4f6
+cksum=675236266

build/pkgs/dateutil/package-version.txt

@@ -1 +1 @@
-2.5.3
+2.8.1

build/pkgs/fplll/debian.txt

@@ -0,0 +1,2 @@
+libfplll-dev
+fplll-tools

build/pkgs/fplll/distros/gentoo.txt

@@ -0,0 +1 @@
+sci-libs/fplll

build/pkgs/fplll/spkg-configure.m4

@@ -0,0 +1,16 @@
+SAGE_SPKG_CONFIGURE([fplll], [
+  SAGE_SPKG_DEPCHECK([mpfr], [
+    dnl If we're using the system mpfr, use pkgconfig to determine
+    dnl if there's a usable system copy of fplll. Unless there's
+    dnl a system that ships fplll without fplll.pc file, falling
+    dnl back to a manual header/library search is pointless.
+    PKG_CHECK_MODULES([FPLLL],
+                      [fplll >= 5.3],
+                      [],
+                      [sage_spkg_install_fplll=yes])
+  ],
+  [ dnl If we're installing sage's mpfr, then we have to install
+    dnl its fplll, too.
+    sage_spkg_install_fplll=yes
+  ])
+])

build/pkgs/gcc/build-gcc

@@ -58,6 +58,8 @@ if [ -n "$LD" -a "$LD" != "ld" ]; then
     CONFIGURE_LD="--with-ld=$LD"
 fi
 
+# Use SAGE_CXX_WITHOUT_STD instead of CXX.
+# This fixes #29162 (gfortran 9.2.0 compile error on debian-jessie with gcc 4.9.2)
 ../src/configure \
     --prefix="$SAGE_LOCAL" \
     --with-local-prefix="$SAGE_LOCAL" \
@@ -67,6 +69,6 @@ fi
     --disable-multilib \
     --disable-nls \
     --disable-libitm \
-    $GCC_CONFIGURE "$CONFIGURE_AS" "$CONFIGURE_LD"
+    $GCC_CONFIGURE "$CONFIGURE_AS" "$CONFIGURE_LD" CXX="$SAGE_CXX_WITHOUT_STD"
 
 sdh_make BOOT_LDFLAGS="-Wl,-rpath,$SAGE_LOCAL/lib"

build/pkgs/gcc/spkg-configure.m4

@@ -94,6 +94,10 @@ SAGE_SPKG_CONFIGURE_BASE([gcc], [
         IS_REALLY_GCC=yes
     fi
 
+    # Save the value of CXX without special flags to enable C++11 support
+    AS_VAR_SET([SAGE_CXX_WITHOUT_STD], [$CXX])
+    AC_SUBST(SAGE_CXX_WITHOUT_STD)
+    # Modify CXX to include an option that enables C++11 support if necessary
     AX_CXX_COMPILE_STDCXX_11([], optional)
     if test $HAVE_CXX11 != 1; then
         SAGE_MUST_INSTALL_GCC([your C++ compiler does not support C++11])

build/pkgs/pyzmq/checksums.ini

@@ -1,4 +1,4 @@
 tarball=pyzmq-VERSION.tar.gz
-sha1=64799b73d6109fb6da5b7deb6101ba13cd7fe885
-md5=3c8039d007bbbd08a2275f52f5dc9a35
-cksum=1455168757
+sha1=b84077344ed67649f34d4af8f619d96acbd03e73
+md5=4650e45ebcf8e08620211c0e720d6066
+cksum=2135729608

build/pkgs/pyzmq/package-version.txt

@@ -1 +1 @@
-18.1.0
+19.0.0

build/pkgs/qepcad/checksums.ini

@@ -1,4 +1,5 @@
 tarball=qepcad-VERSION.tar.gz
-sha1=085f7063811d160b427d6cd92a3e92aaa580030f
-md5=b426b8698ac2e012e2534af9634d743f
-cksum=207677138
+sha1=7de9ff3a7ce61e751d91fe5e74079a706174e4fa
+md5=61ebb23f407a72cee6142a3b144dea06
+cksum=2428332890
+upstream_url=http://www.usna.edu/Users/cs/wcbrown/qepcad/INSTALL/qepcad-VERSION.tar.gz

build/pkgs/qepcad/package-version.txt

@@ -1 +1 @@
-B.1.71
+B.1.72

build/pkgs/qepcad/patches/0001-Don-t-use-timer_t-on-macOS.patch

@@ -0,0 +1,34 @@
+From cc535b88a2ac93fdd390a7ef8ab6005d7a3cd8a0 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Thu, 22 Aug 2019 22:18:17 -0400
+Subject: [PATCH 1/2] Don't use timer_t on macOS
+
+---
+ source/main/MAIN.c | 4 ++++
+ 1 file changed, 4 insertions(+)
+
+diff --git a/source/main/MAIN.c b/source/main/MAIN.c
+index 723306d..73f8cef 100644
+--- a/source/main/MAIN.c
++++ b/source/main/MAIN.c
+@@ -81,6 +81,9 @@ static void init_SIGINT_handler()
+
+ static int sendSignalAfterInterval(int seconds, int signum)
+ {
++#ifdef __APPLE__
++  return 1;
++#else
+   /* Create timer */
+   timer_t timerid;
+   struct sigevent sev;
+@@ -100,6 +103,7 @@ static int sendSignalAfterInterval(int seconds, int signum)
+     return 2;
+
+   return 0;
++#endif
+ }
+
+ int main(int argc, char **argv)
+-- 
+2.19.0
+

build/pkgs/qepcad/patches/0002-WIP-Don-t-add-lrt.patch

@@ -0,0 +1,49 @@
+From 9fa8ce43a1ebbc1807528acf7d109abc19ba3ba4 Mon Sep 17 00:00:00 2001
+From: Matthias Koeppe <mkoeppe@math.ucdavis.edu>
+Date: Thu, 22 Aug 2019 22:39:21 -0400
+Subject: [PATCH 2/2] WIP: Don't add -lrt
+
+---
+ source/Makefile | 12 ++++++++++--
+ 1 file changed, 10 insertions(+), 2 deletions(-)
+
+diff --git a/source/Makefile b/source/Makefile
+index d184650..f13113b 100644
+--- a/source/Makefile
++++ b/source/Makefile
+@@ -30,6 +30,14 @@ SPECIFLAGS =	-I/opt/sfw/include
+ SPECLFLAGS =	-lcurses # on solaris you have to link curses to get readline!
+ endif
+
++LIBS = -lreadline
++
++# On macOS, librt is not available,
++# see https://trac.sagemath.org/ticket/28388
++#ifeq ($(findstring darwin,${OSTYPE}),)
++#LIBS += -lrt
++#endif
++
+ # ============================================================
+ #     Do not touch below unless you know what you are doing
+ # ============================================================
+@@ -44,7 +52,7 @@ EXTLIBS   =	${qe}/extensions/sfext/sfexto.a \
+ 		${qe}/extensions/adj2d/adj2do.a \
+ 		${qe}/extensions/rend/rendo.a \
+ 		${saclib}/lib/saclibo.a \
+-		-lreadline -lrt \
++		$(LIBS) \
+ 		${SPECLFLAGS}
+
+
+@@ -54,7 +62,7 @@ EXTLIBSD  =	${qe}/extensions/sfext/sfextd.a \
+ 		${qe}/extensions/adj2d/adj2dd.a \
+ 		${qe}/extensions/rend/rendd.a \
+ 		${saclib}/lib/saclibd.a \
+-		-lreadline -lrt \
++		$(LIBS) \
+ 		${SPECLFLAGS}
+
+ NAME      =  qepcad
+-- 
+2.19.0
+

build/pkgs/qepcad/patches/qepcad-B-destructor.patch

@@ -0,0 +1,125 @@
+--- a/extensions/rend/Rend_Sample.cc.orig	2018-01-25 14:25:22.000000000 -0700
++++ b/extensions/rend/Rend_Sample.cc	2018-08-29 20:07:27.087257552 -0600
+@@ -40,11 +40,6 @@ Rend_Sample_1DS::Rend_Sample_1DS(Word C,
+ }
+
+
+-Rend_Sample_1DS::~Rend_Sample_1DS()
+-{
+-  
+-}
+-
+ /*************************************************************
+  **  Refines I to 2^k or less, and returns binary rational 
+  **  middle of interval.
+@@ -112,13 +107,6 @@ Rend_Sample_1DO::Rend_Sample_1DO(Rend_Ce
+   L.W = NIL;
+ }
+
+-
+-Rend_Sample_1DO::~Rend_Sample_1DO()
+-{
+-  
+-}
+-
+-
+ Word Rend_Sample_1DO::coordinate(int k)
+ {
+   Word e,j1,j2,J,kp = k;
+@@ -178,11 +166,6 @@ Rend_Sample_2DS::Rend_Sample_2DS(Word C)
+ }
+
+
+-Rend_Sample_2DS::~Rend_Sample_2DS()
+-{
+-  
+-}
+-
+ /*************************************************************
+  **  Refines I to 2^k or less, and returns binary rational 
+  **  lower endpoint.
+@@ -237,11 +220,6 @@ Rend_Sample_2DC::Rend_Sample_2DC(Word C,
+
+ }
+
+-Rend_Sample_2DC::~Rend_Sample_2DC()
+-{
+-  
+-}
+-
+ Word Rend_Sample_2DC::coordinate(int k)
+ {
+   return L.W;
+@@ -265,11 +243,6 @@ Rend_Sample_BR::Rend_Sample_BR(Word a)
+   N.W = a;
+ }
+
+-Rend_Sample_BR::~Rend_Sample_BR()
+-{
+-  
+-}
+-
+ Word Rend_Sample_BR::coordinate(int k)
+ {
+   return N.W;
+--- a/extensions/rend/Rend_Sample.h.orig	2018-01-25 14:25:22.000000000 -0700
++++ b/extensions/rend/Rend_Sample.h	2018-08-29 20:07:27.087257552 -0600
+@@ -32,7 +32,7 @@ class Rend_Sample
+   virtual Word coordinate(int k) = 0; 
+   virtual Word round(int k,int roundup)
+     { return this -> coordinate(k); }
+-  //  virtual ~Rend_Sample() = 0;
++  virtual ~Rend_Sample() {}
+ };
+
+ class Rend_Sample_1DS : public Rend_Sample
+@@ -49,7 +49,6 @@ private:
+   gcmemloc A,I;
+ public:
+   Rend_Sample_1DS(Word C, Word P);
+-  virtual ~Rend_Sample_1DS();
+   virtual Word coordinate(int k);
+   virtual Word round(int k, int roundup);
+   Word weakcompare(Word R);
+@@ -66,7 +65,6 @@ public:
+   gcmemloc L;
+ public:
+   Rend_Sample_1DO(Rend_Cell *dad);
+-  virtual ~Rend_Sample_1DO();
+   virtual Word coordinate(int k);
+
+ };
+@@ -86,7 +84,6 @@ private:
+   gcmemloc A,I;
+ public:
+   Rend_Sample_2DS(Word C);
+-  virtual ~Rend_Sample_2DS();
+   virtual Word coordinate(int k);
+
+ };
+@@ -101,7 +98,6 @@ public:
+   gcmemloc L;
+ public:
+   Rend_Sample_2DC(Word C,Word P);
+-  virtual ~Rend_Sample_2DC();
+   virtual Word coordinate(int k);
+   void add_point(Word p);
+   void clear_points();
+@@ -116,7 +112,6 @@ private:
+   gcmemloc N;
+ public:
+   Rend_Sample_BR(Word a);
+-  virtual ~Rend_Sample_BR();
+   virtual Word coordinate(int k);    
+ };
+
+--- a/plot2d/plot.cc.orig	2018-01-25 14:25:22.000000000 -0700
++++ b/plot2d/plot.cc	2018-08-29 20:07:27.086257553 -0600
+@@ -37,6 +37,7 @@ class CADELT
+ public:
+   virtual bool read(istream &in) = 0;
+   virtual void glRend(const CADColors &C) = 0;
++  virtual ~CADELT() {}
+ };
+
+ class SNoverSR : public CADELT

build/pkgs/qepcad/patches/qepcad-B-env.patch

@@ -0,0 +1,12 @@
+--- a/source/main/BEGINQEPCAD.c.orig	2018-01-30 14:04:58.000000000 -0700
++++ b/source/main/BEGINQEPCAD.c	2018-08-29 20:03:05.718540333 -0600
+@@ -127,7 +127,8 @@ void BEGINQEPCAD(int &argc, char**& argv
+ void QEPCAD_ProcessRC(int argc, char **argv)
+ {
+   char *qepath = getenv("qe");
+-  if (qepath == NULL) { FAIL("QEPCAD_ProcessRC","Environment variable qe not defined!"); }
++  if (qepath == NULL) { setenv("qe", "/usr/share/qepcad", 1); qepath = getenv("qe"); }
++  if (getenv("SINGULARPATH") == NULL) { setenv("SINGULARPATH", "@LIBDIR@/Singular", 1); }
+   string rcFileName = qepath + string("/default.qepcadrc");
+   ifstream rcin(rcFileName.c_str());
+   if (!rcin) { return; }