port Sage to FreeBSD 11

[dimpase]

Please see #26249 for the followup (for FreeBSD 12).

FreeBSD as of version 10 uses clang by default, and is closer to OSX in other ways too, so it would be a good free testing ground for the use of clang with Sage.

preparing tools:

• install gcc6 and create fake gfortran by making a link to gfortran6
• make sure as is new enough: pkg install binutils will install as version 2.28, and you need it to come first in PATH (i.e. make sure that /usr/local/bin comes before /usr/bin).
• remove stale /lib/libgcc_s.so.1 and point it to the right one in /usr/local/lib/gcc6/ (perhaps there is a better way...)
• install gmake, gawk, gsed, and create fake make and sed to point to gmake and gsed
• make sure /bin/sh is actually bash
• install pkgconf (FreeBSD's replacement of pkg-config)
• install wget (needed for AtlasRep GAP package).
• install icu (needed for R)

building Sage itself

starting from a clean git repo:

export CFLAGS="-fPIC"
export CXXFLAGS="-fPIC"
export LDFLAGS="-L/usr/local/lib -Wl,--add-needed -lm"
./configure CC=cc CXX=c++  #(this is clang 3.8.0 a.t.m.)
MAKE="make -j7" make build
MAKE="make -j4" make # building docs is very memory-hungry

HISTORICAL: Sage itself:

• hack configure.ac to make freebsd allowed platform
• deal with cephes' complex.h conflicting with numpy - cephes' complex.h conflicts with a numpy header on FreeBSD #22786
• gf2x: only builds with SAGE_FAT_BINARY on
• upgrade sqlite to version 3.17 - otherwise there are compiling problems with editline (see update sqlite to version 3.17 #22687)
• flint: remove "-ascii -pedantic" flags from CFLAGS in configure
• libraries (libgap, cddlib, etc) need -fPIC for CFLAGS (so we build with CC="cc -fPIC -pipe" ; (-pipe is probably not really needed)) - see on clang libgap needs -fPIC #22784
• but gap cannot be built with CC="cc -fPIC -pipe", as it does something weird in ./configure, setting BASECC to be cc, and generating broken Makefile (with -fPIC and -pipe on two separate lines); so build gap with CC=cc
• giac needs CFLAGS="-I/usr/local/include" to find libintl.h and LDFLAGS="-L/usr/local/lib -lintl" to link.
• either provide /bin/bash or fix this properly (get rid of /bin/bash #22689)
• Sage builds and runs, modulo linking issues with flint and arb, which can be fixed ad hoc by hand.
• deal with cephes' libm not pulling system's libm, unless some arcane linker flags are used (see comments below)
• old freebsd workaround for libgd removed in remove obsolete FreeBSD workaround in libgd #22785
• ...

Depends on #12426
Depends on #23700

CC: @sagetrac-stephen @kiwifb @jdemeyer @jpflori

Component: porting: BSD

Author: Dima Pasechnik

Branch/Commit: u/dimpase/fbsd-support @ 4aaeeb4

Reviewer: Dima Pasechnik

Issue created by migration from https://trac.sagemath.org/ticket/22679

[dimpase]

Description changed:

--- 
+++ 
@@ -5,7 +5,7 @@
 * install gcc6 and create fake gfortran by making a link to gcc6
 * install gmake, gawk, gsed, and create fake make and sed to point to gmake and gsed
 * make sure /bin/sh is actually bash
-* hack configure.ac to make freebsd applowed platform
+* hack configure.ac to make freebsd allowed platform
 * get rid of cephes - it causes linking problems with libm, and is probably not needs any more anyway
 * figure out what to do with Sage's libz and libbz - they cause linking problems (needless to say, 
 * gf2x only builds with SAGE_FAT_BINARY on

[dimpase]

Description changed:

--- 
+++ 
@@ -9,4 +9,5 @@
 * get rid of cephes - it causes linking problems with libm, and is probably not needs any more anyway
 * figure out what to do with Sage's libz and libbz - they cause linking problems (needless to say, 
 * gf2x only builds with SAGE_FAT_BINARY on
+* upgrade sqlite to version 3.17 - otherwise there are compiling problems with editline
 * ...

[dimpase]

Description changed:

--- 
+++ 
@@ -5,9 +5,13 @@
 * install gcc6 and create fake gfortran by making a link to gcc6
 * install gmake, gawk, gsed, and create fake make and sed to point to gmake and gsed
 * make sure /bin/sh is actually bash
+* install pkgconf (FreeBSD's replacement of pkg-config)
 * hack configure.ac to make freebsd allowed platform
 * get rid of cephes - it causes linking problems with libm, and is probably not needs any more anyway
 * figure out what to do with Sage's libz and libbz - they cause linking problems (needless to say, 
-* gf2x only builds with SAGE_FAT_BINARY on
+* gf2x: only builds with SAGE_FAT_BINARY on
 * upgrade sqlite to version 3.17 - otherwise there are compiling problems with editline
+* flint: remove "-ascii -pedantic" flags from CFLAGS in configure
+* libgap: needs -fPIC for CFLAGS
 * ...
+ 

[dimpase]

Description changed:

--- 
+++ 
@@ -1,14 +1,19 @@
 FreeBSD as of version 10 uses clang by default, and is closer to OSX in other ways too, so it would be a good free testing ground for the use of clang with Sage. 
 
 Few details I figured out.
+
+\# preparing tools:
 
 * install gcc6 and create fake gfortran by making a link to gcc6
 * install gmake, gawk, gsed, and create fake make and sed to point to gmake and gsed
 * make sure /bin/sh is actually bash
 * install pkgconf (FreeBSD's replacement of pkg-config)
+
+\# Sage itself:
+
 * hack configure.ac to make freebsd allowed platform
 * get rid of cephes - it causes linking problems with libm, and is probably not needs any more anyway
-* figure out what to do with Sage's libz and libbz - they cause linking problems (needless to say, 
+* figure out what to do with Sage's libz and libbz - they cause linking problems (needless to say, system versions are perfectly good) 
 * gf2x: only builds with SAGE_FAT_BINARY on
 * upgrade sqlite to version 3.17 - otherwise there are compiling problems with editline
 * flint: remove "-ascii -pedantic" flags from CFLAGS in configure

[dimpase]

Description changed:

--- 
+++ 
@@ -2,14 +2,15 @@
 
 Few details I figured out.
 
-\# preparing tools:
+
+## preparing tools:
 
 * install gcc6 and create fake gfortran by making a link to gcc6
 * install gmake, gawk, gsed, and create fake make and sed to point to gmake and gsed
 * make sure /bin/sh is actually bash
 * install pkgconf (FreeBSD's replacement of pkg-config)
 
-\# Sage itself:
+## Sage itself:
 
 * hack configure.ac to make freebsd allowed platform
 * get rid of cephes - it causes linking problems with libm, and is probably not needs any more anyway
@@ -17,6 +18,6 @@
 * gf2x: only builds with SAGE_FAT_BINARY on
 * upgrade sqlite to version 3.17 - otherwise there are compiling problems with editline
 * flint: remove "-ascii -pedantic" flags from CFLAGS in configure
-* libgap: needs -fPIC for CFLAGS
+* libraries (libgap, cddlib, etc) need -fPIC for CFLAGS (so we build with CC="cc -fPIC -pipe" ; (-pipe is probably not really needed))
 * ...
  

[dimpase]

comment:6

cf my comments at
numpy/numpy#8530

for the need for /lib/libgcc_s.so.1 to be replaced.

Basically, gcc/gfortran and clang's toolchains are slightly incompatible; while workarounds are in place for OSX,
linking on freebsd makes it more or less mandatory.

[dimpase]

Description changed:

--- 
+++ 
@@ -5,7 +5,8 @@
 
 ## preparing tools:
 
-* install gcc6 and create fake gfortran by making a link to gcc6
+* install gcc6 and create fake gfortran by making a link to gfortran6
+* remove stale /lib/libgcc_s.so.1 and point it to the right one in /usr/local/lib/gcc6/
 * install gmake, gawk, gsed, and create fake make and sed to point to gmake and gsed
 * make sure /bin/sh is actually bash
 * install pkgconf (FreeBSD's replacement of pkg-config)

[dimpase]

Description changed:

--- 
+++ 
@@ -20,5 +20,6 @@
 * upgrade sqlite to version 3.17 - otherwise there are compiling problems with editline
 * flint: remove "-ascii -pedantic" flags from CFLAGS in configure
 * libraries (libgap, cddlib, etc) need -fPIC for CFLAGS (so we build with CC="cc -fPIC -pipe" ; (-pipe is probably not really needed))
+* giac needs `CFLAGS="-I/usr/local/include"` to find `libintl.h`.
 * ...
  

[dimpase]

comment:9

one of internal giac tests fail (harmlessly, I hope):

< -sqrt(6)*I*sqrt(sqrt(13)+3),sqrt(6)*I*sqrt(sqrt(13)+3),-sqrt(6)*sqrt(sqrt(13)-3),sqrt(6)*sqrt(sqrt(13)-3),0,
---
> sqrt(6)*I*sqrt(sqrt(13)+3),-sqrt(6)*I*sqrt(sqrt(13)+3),-sqrt(6)*sqrt(sqrt(13)-3),sqrt(6)*sqrt(sqrt(13)-3),0,
FAIL: chk_fhan16

[dimpase]

Description changed:

--- 
+++ 
@@ -20,6 +20,7 @@
 * upgrade sqlite to version 3.17 - otherwise there are compiling problems with editline
 * flint: remove "-ascii -pedantic" flags from CFLAGS in configure
 * libraries (libgap, cddlib, etc) need -fPIC for CFLAGS (so we build with CC="cc -fPIC -pipe" ; (-pipe is probably not really needed))
-* giac needs `CFLAGS="-I/usr/local/include"` to find `libintl.h`.
+* giac needs `CFLAGS="-I/usr/local/include"` to find `libintl.h`
+and `LDFLAGS="-L/usr/local/lib -lintl"` to link.
 * ...