error rebuilding sage

[jhonrubia6]

after make dist-clean && make I've got an error compiling atlas-3.10.2. Any ideas, other than re-cloning the sources?

Setting up build directory for atlas-3.10.2

Finished set up

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

Host system:

Darwin OnoSendaiII.local 15.3.0 Darwin Kernel Version 15.3.0: Thu Dec 10 18:40:58 PST 2015; root:xnu-3248.30.4~1/RELEASE_X86_64 x86_64

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

C compiler: gcc

C compiler version:

Configured with: --prefix=/Library/Developer/CommandLineTools/usr --with-gxx-include-dir=/usr/include/c++/4.2.1

Apple LLVM version 7.0.2 (clang-700.1.81)

Target: x86_64-apple-darwin15.3.0

Thread model: posix

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

Cannot execute fortran compiler ($FC)!

real    0m0.071s

user    0m0.041s

sys     0m0.026s

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

Error installing package atlas-3.10.2

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

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

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

  /Users/J_Honrubia/Sage/sage-6.10/sage/logs/pkgs/atlas-3.10.2.log

Describe your computer, operating system, etc.

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

/Users/J_Honrubia/Sage/sage-6.10/sage/local/var/tmp/sage/build/atlas-3.10.2 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 '/Users/J_Honrubia/Sage/sage-6.10/sage/local/var/tmp/sage/build/atlas-3.10.2' && '/Users/J_Honrubia/Sage/sage-6.10/sage/sage' --sh)

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

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

make[1]: *** [/Users/J_Honrubia/Sage/sage-6.10/sage/local/var/lib/sage/installed/atlas-3.10.2] Error 1

real    6m27.702s

user    4m16.457s

sys     1m55.716s

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

Error building Sage.

The following package(s) may have failed to build:

package: atlas-3.10.2

log file: /Users/J_Honrubia/Sage/sage-6.10/sage/logs/pkgs/atlas-3.10.2.log

build directory: /Users/J_Honrubia/Sage/sage-6.10/sage/local/var/tmp/sage/build/atlas-3.10.2

[Volker Braun]

On Wednesday, February 3, 2016 at 6:25:46 PM UTC+1, jhonrubia6 wrote:

after make dist-clean && make I've got an error 

its "make distclean" 

[jhonrubia6]

I'm sorry, it's a typo when writing this message.

Anyway, I tried again, and now it's compiling ok. I do not really know why. 

[jhonrubia6]

... and the new error  (on make distclean && make) is 

/Users/J_Honrubia/Sage/sage-6.10/sage/build/pipestatus "sage-spkg -f setuptools-12.4 2>&1" "tee -a /Users/J_Honrubia/Sage/sage-6.10/sage/logs/pkgs/setuptools-12.4.log"

/Users/J_Honrubia/Sage/sage-6.10/sage/src/bin/sage-env: line 434: /Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/R/share/Makevars.site: No such file or directory

Found local metadata for setuptools-12.4

Attempting to download package setuptools-12.4.tar.gz from mirrors

Downloading the Sage mirror list

Traceback (most recent call last):

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/src/bin/sage-download-file", line 457, in <module>

    tarball.download()

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/src/bin/sage-download-file", line 392, in download

    for mirror in MirrorList():

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/src/bin/sage-download-file", line 152, in __init__

    with contextlib.closing(urllib.urlopen(self.URL)) as f:

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/python/urllib.py", line 87, in urlopen

    return opener.open(url)

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/python/urllib.py", line 213, in open

    return getattr(self, name)(url)

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/python/urllib.py", line 350, in open_http

    h.endheaders(data)

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/python/httplib.py", line 997, in endheaders

    self._send_output(message_body)

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/python/httplib.py", line 850, in _send_output

    self.send(msg)

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/python/httplib.py", line 812, in send

    self.connect()

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/python/httplib.py", line 793, in connect

    self.timeout, self.source_address)

  File "/Users/J_Honrubia/Sage/sage-6.10/sage/local/lib/python/socket.py", line 555, in create_connection

    for res in getaddrinfo(host, port, 0, SOCK_STREAM):

IOError: [Errno socket error] [Errno 8] nodename nor servname provided, or not known

make[2]: *** [/Users/J_Honrubia/Sage/sage-6.10/sage/local/var/lib/sage/installed/setuptools-12.4] Error 1

make[1]: *** [all] Error 2

real 729m8.876s

user 123m22.857s

sys 17m48.141s

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

Error building Sage.

The following package(s) may have failed to build:

The build directory may contain configuration files and other potentially

helpful information. WARNING: if you now run 'make' again, the build

directory will, by default, be deleted. Set the environment variable

SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make: *** [all] Error 1

O

[Dima Pasechnik]

did the internet connection from the machine die during the build, or perhaps you are behind some big bad firewall?

[jhonrubia6]

As the compilation dos through the night, maybe there was some internet downtime that I am not aware of. I will try again and keep track of the router log, thank you for your help

[jhonrubia6]

I passed that point and now fails building ecm,... 

I do not understand what I am making wrong. I had a working installation on 7.0, then after checking out a ticket to review (#18408)I tried to build again and I'm having a lot of problems to get the installation working again

Now building GMP-ECM...

make  all-recursive

Making all in x86_64

m4 -I../ -DOPERATION_mulredc1 `test -f mulredc1.asm || echo './'`mulredc1.asm >mulredc1.s

/bin/sh ../libtool   --mode=compile gcc  -march=native -g -O3  -fPIC -c -o mulredc1.lo mulredc1.s

libtool: compile:  gcc -march=native -g -O3 -fPIC -c mulredc1.s -o mulredc1.o

m4 -I../ -DOPERATION_mulredc2 `test -f mulredc2.asm || echo './'`mulredc2.asm >mulredc2.s

/bin/sh ../libtool   --mode=compile gcc  -march=native -g -O3  -fPIC -c -o mulredc2.lo mulredc2.s

libtool: compile:  gcc -march=native -g -O3 -fPIC -c mulredc2.s -o mulredc2.o

mulredc2.s:40:8: error: invalid alignment value

.align 64 # Opteron L1 code cache line is 64 bytes long

       ^

mulredc2.s:150:8: error: invalid alignment value

.align 32,,16

       ^

make[5]: *** [mulredc2.lo] Error 1

rm mulredc2.s mulredc1.s

make[4]: *** [all-recursive] Error 1

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

Error building GMP-ECM.

real 0m20.742s

user 0m8.886s

sys 0m8.923s

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

Error installing package ecm-6.4.4

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

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

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

  /Users/J_Honrubia/Sage/sage-6.10/sage/logs/pkgs/ecm-6.4.4.log

Describe your computer, operating system, etc.

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

/Users/J_Honrubia/Sage/sage-6.10/sage/local/var/tmp/sage/build/ecm-6.4.4 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 '/Users/J_Honrubia/Sage/sage-6.10/sage/local/var/tmp/sage/build/ecm-6.4.4' && '/Users/J_Honrubia/Sage/sage-6.10/sage/sage' --sh)

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

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

make[2]: *** [/Users/J_Honrubia/Sage/sage-6.10/sage/local/var/lib/sage/installed/ecm-6.4.4] Error 1

make[1]: *** [all] Error 2

real 0m22.540s

user 0m9.866s

sys 0m9.371s

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

Error building Sage.

The following package(s) may have failed to build:

package: ecm-6.4.4

log file: /Users/J_Honrubia/Sage/sage-6.10/sage/logs/pkgs/ecm-6.4.4.log

build directory: /Users/J_Honrubia/Sage/sage-6.10/sage/local/var/tmp/sage/build/ecm-6.4.4

The build directory may contain configuration files and other potentially

helpful information. WARNING: if you now run 'make' again, the build

directory will, by default, be deleted. Set the environment variable

SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.

make: *** [all] Error 1

El jueves, 4 de febrero de 2016, 17:36:46 (UTC+1), Dima Pasechnik escribió:

[Jeroen Demeyer]

On 2016-02-04 19:32, jhonrubia6 wrote:
> I passed that point and now fails building ecm,...
> I do not understand what I am making wrong. I had a working installation
> on 7.0, then after checking out a ticket to review (#18408)I tried to
> build again and I'm having a lot of problems to get the installation
> working again

This should be fixed by
http://trac.sagemath.org/ticket/19233

Which version of Sage is that?

[Volker Braun]

Just to point out the obvious: If you check out #18408 then you get Sage-6.8.beta7

You should merge in the latest Sage if you want to review that ticket; Its likely that there are merge conflicts anyways which need to be resolved first.

[jhonrubia6]

Ok, that explains it (I keep learning, even the obvious). So if I understand correctly I should have merged first, before rebuilding the source. Now, it seems there is no  way back I guess, other than getting a new copy of the source code.

How do I know the version of a given ticket which needs review?

[Dima Pasechnik]

On Thursday, 4 February 2016 21:00:03 UTC, jhonrubia6 wrote:

Ok, that explains it (I keep learning, even the obvious). So if I understand correctly I should have merged first, before rebuilding the source. Now, it seems there is no  way back I guess, other than getting a new copy of the source code.

How do I know the version of a given ticket which needs review?

typically for reviewing you don't even want to know, just merge over the current develop branch.

(or use git trac)

anyhow, if you don't want to check out the branch, 

on the ticket click on "Commits" next to "branch", and then on "Summary"

e.g. for this ticket you will come to

http://git.sagemath.org/sage.git/?h=a9a45bf4314373cda000c34cf8296b457acb5fde

Then in "Age" section you will see: 

Updated Sage version to 6.8.beta7

[Jeroen Demeyer]

On 2016-02-04 22:00, jhonrubia6 wrote:
> How do I know the version of a given ticket which needs review?

Checkout the branch and run "cat VERSION.txt"

[Clemens Heuberger]

On 2016-02-04 23:25, Dima Pasechnik wrote:
>
>
> On Thursday, 4 February 2016 21:00:03 UTC, jhonrubia6 wrote:
>
> How do I know the version of a given ticket which needs review?
>
>
> typically for reviewing you don't even want to know, just merge over the current
> develop branch.
> (or use git trac)

I tend to review tickets in their own sage version (I have a bunch of versions
checked out and compiled) because then adding a reviewer commit is easier.

I have a look at the results of the patchbots, if they can compile and doctest
the ticket on the newest sage version, then I do not check the same thing on my
machine.

>
> anyhow, if you don't want to check out the branch,
> on the ticket click on "Commits" next to "branch", and then on "Summary"
> e.g. for this ticket you will come to
> http://git.sagemath.org/sage.git/?h=a9a45bf4314373cda000c34cf8296b457acb5fde
> Then in "Age" section you will see:
> Updated Sage version to 6.8.beta7

$ git trac fetch 18408
remote branch: public/18408

Von git://trac.sagemath.org/sage
* branch public/18408 -> FETCH_HEAD

$ git describe FETCH_HEAD
6.8.beta7-3-ga9a45bf

so 18408 is 3 commits ahead of 6.8.beta7.

[jhonrubia6]

So, if I understand you correctly, say I have sage 7.0 on my machine and try to review some old ticket, do you recommend me to merge the ticket branch with my copy 

git merge tiket_branch

and then review it?
If the ticket does not compile ok for whatever reason, there will be no way to get rid of it on my copy or am I wrong?

El jueves, 4 de febrero de 2016, 21:49:36 (UTC+1), Volker Braun escribió:

[Jeroen Demeyer]

On 2016-02-06 10:28, jhonrubia6 wrote:
> So, if I understand you correctly, say I have sage 7.0 on my machine and
> try to review some old ticket, do you recommend me to merge the ticket
> branch with my copy

I don't know what you mean with "my copy". Anyway, merging with a more
recent version of Sage (preferably the latest beta) is indeed a good
thing to do.

[jhonrubia6]

I meant my local copy of the source code. 

Ok. I will proceed as you say, thank you all

[Dima Pasechnik]

On Saturday, February 6, 2016 at 9:28:36 AM UTC, jhonrubia6 wrote:

So, if I understand you correctly, say I have sage 7.0 on my machine and try to review some old ticket, do you recommend me to merge the ticket branch with my copy 

git merge tiket_branch

and then review it?
If the ticket does not compile ok for whatever reason, there will be no way to get rid of it on my copy or am I wrong?

# this is how to do this with plain git:

 

git checkout -b tiket_brunch develop

# now we are on a copy of develop, called tiket_brunch (or whatever)

git fetch trac tiket_brunch

git merge FETCH_HEAD

# now we have merged branch from trac into tiket_brunch

# now do make test stuff, etc

git checkout develop

make

# now we are back to our develop

# (you can now remove your local tiket_brunch using appropriate git commands)

[Travis Scrimshaw]

 

git fetch trac tiket_brunch

git merge FETCH_HEAD

This could also just be done by

git pull trac tiket_brunch

Best,
Travis