Sage 7.0 released

[Volker Braun]

The "master" git branch has been updated to Sage-7.0. As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html

As a final reminder, there are no incremental updates from 6.x to 7.0: You have to recompile all of Sage (make distclean && make)

1961f94 Updated Sage version to 7.0

94dd2e2 Trac #19843: Improve location change error message

858e8d9 Trac #19879: Move sage/rings/arith to sage/arith

c857bbc Trac #19415: Deprecate composite_field()

adef4de Updated Sage version to 7.0.rc1

[Emmanuel Charpentier]

FWIW, passes ptestlong with no errors on Debian testing rinning on CoreI7+16GB RAM. Idem for 7.0+Trac#19851+Trac#19885.

--
Emmanuel Charpentier

[Volker Braun]

The binaries are now on the file server

[Harald Schilly]

Great! I've pushed the version number on the website and the timestamp on files.

-- harald

On Sat, Jan 23, 2016 at 7:13 PM, Volker Braun <vbrau...@gmail.com> wrote:
> The binaries are now on the file server
>

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[kcrisman]

Untested is broken:

http://ask.sagemath.org/question/32330/sage-notebook-is-not-working/

This is via the .app bundle, I think.  What could have changed to make this not work? 

[Dima Pasechnik]

is it notebook-specfic, or a not working OSX binary?

[kcrisman]

Untested is broken:

http://ask.sagemath.org/question/32330/sage-notebook-is-not-working/

This is via the .app bundle, I think.  What could have changed to make this not work? 

is it notebook-specfic, or a not working OSX binary?

It seems to be that the notebook doesn't import sage.all. Although a new comment here says

Yes, sage from sage-7.0-osx-10.11.2-x86_64.app.dmg as well as sage from the sage-7.0-osx-10.11.2-x86_64.dmg do not import "sage.all". They return an import error on cliquer.so even though the library exists.

so maybe it's related to that issue instead, hence not universal?

[Volker Braun]

I've deleted the Sage-7.0 OSX binaries

[kcrisman]

I've deleted the Sage-7.0 OSX binaries

 Are there any processors we are sure they work on?  I guess in theory one could just say on the download page "use with > 2014 computers else use 6.10" but maybe that's more trouble than it's worth.

[Justin C. Walker]

On Jan 19, 2016, at 06:21 , Volker Braun wrote:

> The "master" git branch has been updated to Sage-7.0. As always, you can
> get the latest beta version from the "develop" git branch. Alternatively,
> the self-contained source tarball is at
> http://www.sagemath.org/download-latest.html

Built (make ptestlong) on three OS X systems:
10.6.8 (Dual 6-core Xeons): build problems - see below
10.10.5 (Quad-core Core i7): no problems; all tests passed.
10.11.3 (Quad-core Core i7): no problems; all tests passed.

The build on 10.6.8 blew up in early going:

sh: /Users/Sage/sage-7.0/build/bin/mv: No such file or directory
make[6]: *** [stripslash.o] Error 127
make[6]: *** Waiting for unfinished jobs....
make[5]: *** [all] Error 2
make[4]: *** [all-recursive] Error 1
make[3]: *** [all] Error 2
Error building GNU patch

real 0m24.921s
user 0m11.104s
sys 0m12.731s
************************************************************************
Error installing package patch-2.7.5
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/Users/Sage/sage-7.0/logs/pkgs/patch-2.7.5.log

I can send the whole log, but it seems the relevant part is the above. Not sure why 'mv' was expected in the Sage tree...

Justin

--
Justin C. Walker, Curmudgeon-at-Large
() The ASCII Ribbon Campaign
/\ Help Cure HTML Email

[Volker Braun]

Is that a parallel build? the mashed-together log isn't very meaningful.

[Justin C. Walker]

On Jan 31, 2016, at 15:23 , Volker Braun wrote:

> Is that a parallel build? the mashed-together log isn't very meaningful.

Yes it is (-j24; Dual 6-core Xeons).

With any luck, you will find a tarball of the logs directory attached.

[Samuel Lelievre]

2016-01-31 23:39:30 Z, Justin C. Walker:

 
I think Volker's question could be expanded into the
following recommendation.

When a parallel build fails, it's good to
- save the log files
- run a non-parallel build.

If the non-parallel build also fails, it will provide
easier-to-analyze logs.

Otherwise, you can report that the failure was
observed with the parallel build but not with
the non-parallel build.

[Justin C. Walker]

Thanks for the suggestion. 'Twould appear that the non-parallel build is successful, at least so far. It's quietly chugging along passing the 18th spkg now. More to come.

Justin

--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------
While creating wives, God promised men
that good and obedient wives would be
found in all corners of the world.
Then He made the earth round.
--

[Justin C. Walker]

> On Jan 19, 2016, at 06:21, Volker Braun <vbrau...@gmail.com> wrote:
>
> The "master" git branch has been updated to Sage-7.0. As always, you can get the latest beta version from the "develop" git branch. Alternatively, the self-contained source tarball is at http://www.sagemath.org/download-latest.html
>
> As a final reminder, there are no incremental updates from 6.x to 7.0: You have to recompile all of Sage (make distclean && make)

Following SLelievre’s suggestion, I reran the build, from scratch, as “make ptestlong”, no parallelism. The build completed, as did the doc build. However, the testing never got started; the doc build seemed to hang at the end.

I tried to repeat this with earlier betas, with the same result, except that for the betas, the “-j24” builds did complete w/o problems (as for the final, the doc builds hung at the end).

More to come as I try to figure out what’s hanging.

This is all on 10.6.8 (Dual 6-core Xeons). Builds on 10.10 and 10.11 work w/o problems with successful testing (‘ptestlong’).

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Director
Institute for the Enhancement of the Director's Income
--------
"Weaseling out of things is what separates us from the animals.
Well, except the weasel."
- Homer J Simpson
--------

[Volker Braun]

Are you sure you are not running out of memory in the doc build? You need > 2gb / process.

[Jean-Philippe Labbé]

A colleague has a error in the compilation of Sage 7.0:

"Error installing package mpc-1.0.3.p0" here is a part of the log file:

****************************************************

dyld: lazy symbol binding failed: Symbol not found: _openat

  Referenced from: /Applications/Sage/sage-7.0/local/bin/patch

  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _openat

  Referenced from: /Applications/Sage/sage-7.0/local/bin/patch

  Expected in: /usr/lib/libSystem.B.dylib

./spkg-install: line 13: 87768 Trace/BPT trap: 5       patch -p1 < "$patch"

Error applying '../patches/mpc_mul_faster.patch'

His computer is a MacBook Air 1.8Ghz Intel Core i5, 8GB RAM OS 10.9.5

[Jeroen Demeyer]

On 2016-03-07 13:35, Jean-Philippe Labbé wrote:
> A colleague has a error in the compilation of Sage 7.0:

First of all, make sure that this colleague downloaded the *source*
tarball of Sage if he wanted to compile from source.

Second, please send the contents of the files
logs/pkgs/patch-2.7.5.log
and
logs/pkgs/mpc-1.0.3.p0.log

[pevde...@gmail.com]

Dear Jeroen,

The tarball I downloaded was source. Below are the last bits of my log files.

Here's my patch-2.7.5.log:

/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(chownat.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(fd-hook.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(gl_list.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(stat-time.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(statat.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(timespec.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(unistd.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(wctype-h.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(gl_xlist.o) has no symbols
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ranlib: file: libpatch.a(xsize.o) has no symbols
GEN charset.alias
GEN ref-add.sed
GEN ref-del.sed
Making all in src
CC inp.o
CC patch.o
patch.c:492:14: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int]
"s" + (in_offset == 1));
~~~~^~~~~~~~~~~~~~~~~~
patch.c:492:14: note: use array indexing to silence this warning
"s" + (in_offset == 1));
^
& [ ]
patch.c:617:55: warning: adding 'int' to a string does not append to the string [-Wstring-plus-int]
say ("%d out of %d hunk%s %s", failed, hunk, "s" + (hunk == 1),
~~~~^~~~~~~~~~~~~
patch.c:617:55: note: use array indexing to silence this warning
say ("%d out of %d hunk%s %s", failed, hunk, "s" + (hunk == 1),
^
& [ ]
2 warnings generated.
CC pch.o
CC safe.o
CC util.o
util.c:562:22: warning: use of logical '&&' with constant operand [-Wconstant-logical-operand]
if (! (O_CREAT && O_TRUNC))
^ ~~~~~~~
util.c:562:22: note: use '&' for a bitwise operation
if (! (O_CREAT && O_TRUNC))
^~
&
util.c:562:22: note: remove constant to silence this warning
if (! (O_CREAT && O_TRUNC))
~^~~~~~~~~~
1 warning generated.
CC version.o
CC merge.o
merge.c:471:35: warning: adding 'bool' to a string does not append to the string [-Wstring-plus-int]
fputs (outstate->after_newline + "\n<<<<<<<\n", fp);
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
merge.c:471:35: note: use array indexing to silence this warning
merge.c:482:39: warning: adding 'bool' to a string does not append to the string [-Wstring-plus-int]
fputs (outstate->after_newline + "\n|||||||\n", fp);
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
merge.c:482:39: note: use array indexing to silence this warning
merge.c:491:35: warning: adding 'bool' to a string does not append to the string [-Wstring-plus-int]
fputs (outstate->after_newline + "\n=======\n", fp);
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
merge.c:491:35: note: use array indexing to silence this warning
merge.c:498:35: warning: adding 'bool' to a string does not append to the string [-Wstring-plus-int]
fputs (outstate->after_newline + "\n>>>>>>>\n", fp);
~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
merge.c:498:35: note: use array indexing to silence this warning
4 warnings generated.
CCLD patch
Making all in tests
make[5]: Nothing to be done for `all'.
make[5]: Nothing to be done for `all-am'.
make install-recursive
Making install in lib
make install-am
if test no = no; then \
case 'darwin13.4.0' in \
darwin[56]*) \
need_charset_alias=true ;; \
darwin* | cygwin* | mingw* | pw32* | cegcc*) \
need_charset_alias=false ;; \
*) \
need_charset_alias=true ;; \
esac ; \
else \
need_charset_alias=false ; \
fi ; \
if $need_charset_alias; then \
/bin/sh /Applications/Sage/sage-7.0/local/var/tmp/sage/build/patch-2.7.5/src/build-aux/install-sh -d /Applications/Sage/sage-7.0/local/lib ; \
fi ; \
if test -f /Applications/Sage/sage-7.0/local/lib/charset.alias; then \
sed -f ref-add.sed /Applications/Sage/sage-7.0/local/lib/charset.alias > /Applications/Sage/sage-7.0/local/lib/charset.tmp ; \
/usr/bin/install -c -m 644 /Applications/Sage/sage-7.0/local/lib/charset.tmp /Applications/Sage/sage-7.0/local/lib/charset.alias ; \
rm -f /Applications/Sage/sage-7.0/local/lib/charset.tmp ; \
else \
if $need_charset_alias; then \
sed -f ref-add.sed charset.alias > /Applications/Sage/sage-7.0/local/lib/charset.tmp ; \
/usr/bin/install -c -m 644 /Applications/Sage/sage-7.0/local/lib/charset.tmp /Applications/Sage/sage-7.0/local/lib/charset.alias ; \
rm -f /Applications/Sage/sage-7.0/local/lib/charset.tmp ; \
fi ; \
fi
make[7]: Nothing to be done for `install-data-am'.
Making install in src
../build-aux/install-sh -c -d '/Applications/Sage/sage-7.0/local/bin'
/usr/bin/install -c patch '/Applications/Sage/sage-7.0/local/bin'
make[6]: Nothing to be done for `install-data-am'.
Making install in tests
make[6]: Nothing to be done for `install-exec-am'.
make[6]: Nothing to be done for `install-data-am'.
make[6]: Nothing to be done for `install-exec-am'.
build-aux/install-sh -c -d '/Applications/Sage/sage-7.0/local/share/man/man1'
/usr/bin/install -c -m 644 'patch.man' '/Applications/Sage/sage-7.0/local/share/man/man1/patch.1'

real 0m57.610s
user 0m30.564s
sys 0m23.142s
Successfully installed patch-2.7.5
Deleting temporary build directory
/Applications/Sage/sage-7.0/local/var/tmp/sage/build/patch-2.7.5
Finished installing patch-2.7.5.spkg








And here's my mpc-1.0.3.p0.log:

====================================================
Setting up build directory for mpc-1.0.3.p0
Finished set up
****************************************************
Host system:
Darwin wpa-24-95.dyn.huji.ac.il 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64
****************************************************
C compiler: /usr/bin/clang
C compiler version:
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

****************************************************
dyld: lazy symbol binding failed: Symbol not found: _openat
Referenced from: /Applications/Sage/sage-7.0/local/bin/patch
Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _openat
Referenced from: /Applications/Sage/sage-7.0/local/bin/patch
Expected in: /usr/lib/libSystem.B.dylib

./spkg-install: line 13: 87768 Trace/BPT trap: 5 patch -p1 < "$patch"
Error applying '../patches/mpc_mul_faster.patch'

real 0m1.026s
user 0m0.004s
sys 0m0.005s
************************************************************************
Error installing package mpc-1.0.3.p0

************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file
/Applications/Sage/sage-7.0/logs/pkgs/mpc-1.0.3.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/Applications/Sage/sage-7.0/local/var/tmp/sage/build/mpc-1.0.3.p0 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/Applications/Sage/sage-7.0/local/var/tmp/sage/build/mpc-1.0.3.p0' && '/Applications/Sage/sage-7.0/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
Found local metadata for mpc-1.0.3.p0
Using cached file /Applications/Sage/sage-7.0/upstream/mpc-1.0.3.tar.gz
mpc-1.0.3.p0
====================================================
Setting up build directory for mpc-1.0.3.p0
Finished set up
****************************************************
Host system:
Darwin Evans-MacBook-Air.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64
****************************************************
C compiler: /usr/bin/clang
C compiler version:
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

****************************************************
dyld: lazy symbol binding failed: Symbol not found: _openat
Referenced from: /Applications/Sage/sage-7.0/local/bin/patch
Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _openat
Referenced from: /Applications/Sage/sage-7.0/local/bin/patch
Expected in: /usr/lib/libSystem.B.dylib

./spkg-install: line 13: 88979 Trace/BPT trap: 5 patch -p1 < "$patch"
Error applying '../patches/mpc_mul_faster.patch'

real 0m0.376s
user 0m0.004s
sys 0m0.005s
************************************************************************
Error installing package mpc-1.0.3.p0

************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file
/Applications/Sage/sage-7.0/logs/pkgs/mpc-1.0.3.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/Applications/Sage/sage-7.0/local/var/tmp/sage/build/mpc-1.0.3.p0 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/Applications/Sage/sage-7.0/local/var/tmp/sage/build/mpc-1.0.3.p0' && '/Applications/Sage/sage-7.0/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
Found local metadata for mpc-1.0.3.p0
Using cached file /Applications/Sage/sage-7.0/upstream/mpc-1.0.3.tar.gz
mpc-1.0.3.p0
====================================================
Setting up build directory for mpc-1.0.3.p0
Finished set up
****************************************************
Host system:
Darwin Evans-MacBook-Air.local 13.4.0 Darwin Kernel Version 13.4.0: Wed Mar 18 16:20:14 PDT 2015; root:xnu-2422.115.14~1/RELEASE_X86_64 x86_64
****************************************************
C compiler: /usr/bin/clang
C compiler version:
Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn)
Target: x86_64-apple-darwin13.4.0
Thread model: posix

****************************************************
dyld: lazy symbol binding failed: Symbol not found: _openat
Referenced from: /Applications/Sage/sage-7.0/local/bin/patch
Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _openat
Referenced from: /Applications/Sage/sage-7.0/local/bin/patch
Expected in: /usr/lib/libSystem.B.dylib

./spkg-install: line 13: 89794 Trace/BPT trap: 5 patch -p1 < "$patch"
Error applying '../patches/mpc_mul_faster.patch'

real 0m0.353s
user 0m0.004s
sys 0m0.005s
************************************************************************
Error installing package mpc-1.0.3.p0

************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file
/Applications/Sage/sage-7.0/logs/pkgs/mpc-1.0.3.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/Applications/Sage/sage-7.0/local/var/tmp/sage/build/mpc-1.0.3.p0 and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/Applications/Sage/sage-7.0/local/var/tmp/sage/build/mpc-1.0.3.p0' && '/Applications/Sage/sage-7.0/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************



thanks for the help!
Evan

[Dima Pasechnik]

the following in your log

>C compiler: /usr/bin/clang 
>C compiler version: 
>Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn) 

looks very strange; Sage is not built using clang...

[Jeroen Demeyer]

On 2016-03-08 13:59, pevde...@gmail.com wrote:
> Dear Jeroen,
>
> The tarball I downloaded was source. Below are the last bits of my log files.

Thanks, but I have no idea what happened.

Just to be sure, could you try

make distclean; make

and see if that changed anything?

[Volker Braun]

The openat(2) was introduced in OSX 10.10, so the error that it cannot be found in libSystem.B.dylib is factual. Can you check that we compile for the right version? Whats the output of:

$ sage -sh

$ echo $MACOSX_DEPLOYMENT_TARGET

We don't have any OSX 10.9 machines to test; In any case Apple abandoned that version with unfixed serious vulnerabilities so I would highly suggest to upgrade.

[Volker Braun]

That is as expected, OSX is building the prerequisites for compiling gcc with clang.

[pevde...@gmail.com]

Dear all,

I've upgraded to OSX 10.11.3 and tried again to compile with make distclean, and then make. The compile still fails but this time with a different error: "Error installing package gcc-4.9.3.p1"

Volker: The output from the commands you gave is 10.9.

Pasted below are the last few lines of my sage-7.0/logs/pkgs/gcc-4.9.3.p1.log.

All the best,

Evan

/usr/bin/clang++ -c   -g  -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wmissing-format-attribute -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common  -DHAVE_CONFIG_H -I. -I. -I../../src/gcc -I../../src/gcc/. -I../../src/gcc/../include -I../../src/gcc/../libcpp/include -I/Applications/Sage/sage-7.0/local/include -I/Applications/Sage/sage-7.0/local/include -I/Applications/Sage/sage-7.0/local/include  -I../../src/gcc/../libdecnumber -I../../src/gcc/../libdecnumber/dpd -I../libdecnumber -I../../src/gcc/../libbacktrace    -o darwin-driver.o -MT darwin-driver.o -MMD -MP -MF ./.deps/darwin-driver.TPo ../../src/gcc/config/darwin-driver.c

clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated

/usr/bin/clang++   -g  -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wmissing-format-attribute -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common  -DHAVE_CONFIG_H -Wl,-no_pie -L/Applications/Sage/sage-7.0/local/lib -Wl,-rpath,/Applications/Sage/sage-7.0/local/lib  -o xgcc gcc.o ggc-none.o \

  c/gccspec.o driver-i386.o darwin-driver.o libcommon-target.a \

  libcommon.a ../libcpp/libcpp.a  -liconv ../libbacktrace/.libs/libbacktrace.a ../libiberty/libiberty.a ../libdecnumber/libdecnumber.a 

/usr/bin/clang++ -c   -g  -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wmissing-format-attribute -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common  -DHAVE_CONFIG_H -I. -Ic-family -I../../src/gcc -I../../src/gcc/c-family -I../../src/gcc/../include -I../../src/gcc/../libcpp/include -I/Applications/Sage/sage-7.0/local/include -I/Applications/Sage/sage-7.0/local/include -I/Applications/Sage/sage-7.0/local/include  -I../../src/gcc/../libdecnumber -I../../src/gcc/../libdecnumber/dpd -I../libdecnumber -I../../src/gcc/../libbacktrace    -o c-family/cppspec.o -MT c-family/cppspec.o -MMD -MP -MF c-family/.deps/cppspec.TPo ../../src/gcc/c-family/cppspec.c

clang: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated

/usr/bin/clang++   -g  -DIN_GCC    -fno-exceptions -fno-rtti -fasynchronous-unwind-tables -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wmissing-format-attribute -pedantic -Wno-long-long -Wno-variadic-macros -Wno-overlength-strings -fno-common  -DHAVE_CONFIG_H -Wl,-no_pie -L/Applications/Sage/sage-7.0/local/lib -Wl,-rpath,/Applications/Sage/sage-7.0/local/lib  -o cpp gcc.o ggc-none.o \

  c-family/cppspec.o driver-i386.o darwin-driver.o libcommon-target.a \

  libcommon.a ../libcpp/libcpp.a  -liconv ../libbacktrace/.libs/libbacktrace.a ../libiberty/libiberty.a ../libdecnumber/libdecnumber.a 

/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/xgcc -B/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/ -dumpspecs > tmp-specs

mv tmp-specs specs

: > tmp-libgcc.mvars

echo GCC_CFLAGS = '-g -O2 -DIN_GCC    -W -Wall -Wno-narrowing -Wwrite-strings -Wcast-qual -Wno-format -Wstrict-prototypes -Wmissing-prototypes -Wold-style-definition  -isystem ./include ' >> tmp-libgcc.mvars

echo INHIBIT_LIBC_CFLAGS = '' >> tmp-libgcc.mvars

echo TARGET_SYSTEM_ROOT = '' >> tmp-libgcc.mvars

mv tmp-libgcc.mvars libgcc.mvars

echo | /Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/xgcc -B/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/ -E -dM - | \

  sed -n -e 's/^#define \([^_][a-zA-Z0-9_]*\).*/\1/p' \

-e 's/^#define \(_[^_A-Z][a-zA-Z0-9_]*\).*/\1/p' | \

  sort -u > tmp-macro_list

/bin/sh ../../src/gcc/../move-if-change tmp-macro_list macro_list

echo timestamp > s-macro_list

if /Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/xgcc -B/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/ -print-sysroot-headers-suffix > /dev/null 2>&1; then \

  set -e; for ml in `/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/xgcc -B/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/ -print-multi-lib`; do \

    multi_dir=`echo ${ml} | sed -e 's/;.*$//'`; \

    flags=`echo ${ml} | sed -e 's/^[^;]*;//' -e 's/@/ -/g'`; \

    sfx=`/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/xgcc -B/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1/gcc-build/./gcc/ ${flags} -print-sysroot-headers-suffix`; \

    if [ "${multi_dir}" = "." ]; \

      then multi_dir=""; \

    else \

      multi_dir=/${multi_dir}; \

    fi; \

    echo "${sfx};${multi_dir}"; \

  done; \

else \

  echo ";"; \

fi > tmp-fixinc_list

/bin/sh ../../src/gcc/../move-if-change tmp-fixinc_list fixinc_list

echo timestamp > s-fixinc_list

rm -rf include-fixed; mkdir include-fixed

chmod a+rx include-fixed

if [ -d ../prev-gcc ]; then \

  cd ../prev-gcc && \

  make real-install-headers-tar DESTDIR=`pwd`/../gcc/ \

    libsubdir=. ; \

else \

  set -e; for ml in `cat fixinc_list`; do \

    sysroot_headers_suffix=`echo ${ml} | sed -e 's/;.*$//'`; \

    multi_dir=`echo ${ml} | sed -e 's/^[^;]*;//'`; \

    fix_dir=include-fixed${multi_dir}; \

    if ! false && test ! -d `echo /usr/include | sed -e :a -e 's,[^/]*/\.\.\/,,' -e ta`; then \

      echo The directory that should contain system headers does not exist: >&2 ; \

      echo "  `echo /usr/include | sed -e :a -e 's,[^/]*/\.\.\/,,' -e ta`" >&2 ; \

      tooldir_sysinc=`echo "/Applications/Sage/sage-7.0/local/lib/gcc/x86_64-apple-darwin15.3.0/4.9.3/../../../../x86_64-apple-darwin15.3.0/sys-include" | sed -e :a -e "s,[^/]*/\.\.\/,," -e ta`; \

      if test "x`echo /usr/include | sed -e :a -e 's,[^/]*/\.\.\/,,' -e ta`" = "x${tooldir_sysinc}"; \

      then sleep 1; else exit 1; fi; \

    fi; \

    /bin/sh ../../src/gcc/../mkinstalldirs ${fix_dir}; \

    chmod a+rx ${fix_dir} || true; \

    (TARGET_MACHINE='x86_64-apple-darwin15.3.0'; srcdir=`cd ../../src/gcc; ${PWDCMD-pwd}`; \

      SHELL='/bin/sh'; MACRO_LIST=`${PWDCMD-pwd}`/macro_list ; \

      gcc_dir=`${PWDCMD-pwd}` ; \

      export TARGET_MACHINE srcdir SHELL MACRO_LIST && \

      cd ../build-x86_64-apple-darwin15.3.0/fixincludes && \

      /bin/sh ./fixinc.sh "${gcc_dir}/${fix_dir}" \

        `echo /usr/include | sed -e :a -e 's,[^/]*/\.\.\/,,' -e ta`  ); \

    rm -f ${fix_dir}/syslimits.h; \

    if [ -f ${fix_dir}/limits.h ]; then \

      mv ${fix_dir}/limits.h ${fix_dir}/syslimits.h; \

    else \

      cp ../../src/gcc/gsyslimits.h ${fix_dir}/syslimits.h; \

    fi; \

    chmod a+r ${fix_dir}/syslimits.h; \

  done; \

fi

The directory that should contain system headers does not exist:

  /usr/include

make[6]: *** [stmp-fixinc] Error 1

make[5]: *** [all-stage1-gcc] Error 2

make[4]: *** [stage1-bubble] Error 2

make[3]: *** [all] Error 2

real 6m28.766s

user 4m59.615s

sys 1m11.163s

************************************************************************

Error installing package gcc-4.9.3.p1

************************************************************************

Please email sage-devel (http://groups.google.com/group/sage-devel)

explaining the problem and including the relevant part of the log file

  /Applications/Sage/sage-7.0/logs/pkgs/gcc-4.9.3.p1.log

Describe your computer, operating system, etc.

If you want to try to fix the problem yourself, *don't* just cd to

/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1 and type 'make' or whatever is appropriate.

Instead, the following commands setup all environment variables

correctly and load a subshell for you to debug the error:

  (cd '/Applications/Sage/sage-7.0/local/var/tmp/sage/build/gcc-4.9.3.p1' && '/Applications/Sage/sage-7.0/sage' --sh)

When you are done debugging, you can type "exit" to leave the subshell.

[Volker Braun]

You don't have the xcode command line tools installed, probably were lost in the OSX update.

[pevde...@gmail.com]

Hi all,

After upgrading the OS and reinstalling command line tools, Sage builds without any issues. Thank you!

Evan