Re: [sage-devel] Build error instructed me to post a message here

['bruno edwards' via sage-devel]

Hi Dima,

My ./configure tells me I have additional packages to install, but
installing them seems not to change anything. e.g. the output from
./configure:





*configure:notice: the following SPKGs did not find equivalent system
packages:appdirs distlib filelock...*

so I apt-get installed appdirs, python3-appdirs and python-appdirs, and
even after successful installation, ./configure still gives the same
message (including appdirs).

I never had these problems initially, but my computer has been acting up
recently, so I think I might reinstall my OS.

Best,

Bruno

On Fri, Nov 4, 2022 at 7:18 PM Dima Pasechnik  wrote:

> avoid building gcc. You don't need it. Read advice on packages printed by
> ./configure at the end of run, and follow it.
>
> I'd give you more details over a teams or google meet call.
> (Bruno is one of our 3rd year students I advise this year).
>
> Dima
>
> On Fri, 4 Nov 2022, 18:29 'bruno edwards' via sage-devel, <
> sage-devel@googlegroups.com> wrote:
>
>> Hi, I've been getting this error when trying to build sage - any ideas?
>>
>> I've tried running the subshell command, but I still get an error - see
>> the attached output.
>>
>> I've also attached my neofetch output containing system specs
>>
>> Thanks in advance,
>>
>> Bruno
>>
>> [gcc-11.3.0]
>> 
>> [gcc-11.3.0] Error building package gcc-11.3.0
>> [gcc-11.3.0]
>> 
>> [gcc-11.3.0] Please email sage-devel (
>> http://groups.google.com/group/sage-devel)
>> [gcc-11.3.0] explaining the problem and including the log files
>> [gcc-11.3.0]   /media/EXTRA_PARTITION/sage/sage/logs/pkgs/gcc-11.3.0.log
>> [gcc-11.3.0] and
>> [gcc-11.3.0]   /media/EXTRA_PARTITION/sage/sage/config.log
>> [gcc-11.3.0] Describe your computer, operating system, etc.
>> [gcc-11.3.0] If you want to try to fix the problem yourself, *don't* just
>> cd to
>> [gcc-11.3.0]
>> /media/EXTRA_PARTITION/sage/sage/local/var/tmp/sage/build/gcc-11.3.0 and
>> type 'make' or whatever is appropriate.
>> [gcc-11.3.0] Instead, the following commands setup all environment
>> variables
>> [gcc-11.3.0] correctly and load a subshell for you to debug the error:
>> [gcc-11.3.0]   (cd
>> '/media/EXTRA_PARTITION/sage/sage/local/var/tmp/sage/build/gcc-11.3.0' &&
>> '/media/EXTRA_PARTITION/sage/sage/sage' --buildsh)
>> [gcc-11.3.0] When you are done debugging, you can type "exit" to leave
>> the subshell.
>> [gcc-11.3.0]
>> 
>>
>> --
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>> "sage-devel" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to sage-devel+unsubscr...@googlegroups.com.
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>> 
>> .
>>
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> 
> .
>

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Re: [sage-devel] Build error instructed me to post a message here

[Dima Pasechnik]

avoid building gcc. You don't need it. Read advice on packages printed by
./configure at the end of run, and follow it.

I'd give you more details over a teams or google meet call.
(Bruno is one of our 3rd year students I advise this year).

Dima

On Fri, 4 Nov 2022, 18:29 'bruno edwards' via sage-devel, <
sage-devel@googlegroups.com> wrote:

> Hi, I've been getting this error when trying to build sage - any ideas?
>
> I've tried running the subshell command, but I still get an error - see
> the attached output.
>
> I've also attached my neofetch output containing system specs
>
> Thanks in advance,
>
> Bruno
>
> [gcc-11.3.0]
> 
> [gcc-11.3.0] Error building package gcc-11.3.0
> [gcc-11.3.0]
> 
> [gcc-11.3.0] Please email sage-devel (
> http://groups.google.com/group/sage-devel)
> [gcc-11.3.0] explaining the problem and including the log files
> [gcc-11.3.0]   /media/EXTRA_PARTITION/sage/sage/logs/pkgs/gcc-11.3.0.log
> [gcc-11.3.0] and
> [gcc-11.3.0]   /media/EXTRA_PARTITION/sage/sage/config.log
> [gcc-11.3.0] Describe your computer, operating system, etc.
> [gcc-11.3.0] If you want to try to fix the problem yourself, *don't* just
> cd to
> [gcc-11.3.0]
> /media/EXTRA_PARTITION/sage/sage/local/var/tmp/sage/build/gcc-11.3.0 and
> type 'make' or whatever is appropriate.
> [gcc-11.3.0] Instead, the following commands setup all environment
> variables
> [gcc-11.3.0] correctly and load a subshell for you to debug the error:
> [gcc-11.3.0]   (cd
> '/media/EXTRA_PARTITION/sage/sage/local/var/tmp/sage/build/gcc-11.3.0' &&
> '/media/EXTRA_PARTITION/sage/sage/sage' --buildsh)
> [gcc-11.3.0] When you are done debugging, you can type "exit" to leave the
> subshell.
> [gcc-11.3.0]
> 
>
> --
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> 
> .
>

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Re: [sage-devel] build error, building current beta on ubuntu

['jambodev' via sage-devel]

Thanks again. I was able to build sage.

On Wednesday, 30 December 2020 at 17:55:12 UTC jambodev wrote:

> Thanks Dima,
>
> I'll remove that and will retry.
>
> cheers,
>
>
> On Wednesday, 30 December 2020 at 16:16:18 UTC dim...@gmail.com wrote:
>
>> in the install.log, one sees 
>>
>> [sagelib-9.3.beta4] /usr/local/include/flint/fmpz_poly_mat.h:105:44: 
>> error: unknown type name ‘flint_bitcnt_t’; did you mean 
>> ‘flint_rand_t’? 
>> [sagelib-9.3.beta4] 105 | slong len, 
>> flint_bitcnt_t bits); 
>> [sagelib-9.3.beta4] | 
>> ^~ 
>> [sagelib-9.3.beta4] | 
>> flint_rand_t 
>> [sagelib-9.3.beta4] /usr/local/include/flint/fmpz_poly_mat.h:108:41: 
>> error: unknown type name ‘flint_bitcnt_t’; did you mean 
>> ‘flint_rand_t’? 
>> [sagelib-9.3.beta4] 108 | slong len, 
>> flint_bitcnt_t bits); 
>>
>> which indicates that you most probably have a conflicting copy of 
>> flint in /usr/local/ 
>> - as well as a copy of a system package flint in /usr/ 
>> (and they are mixed up in the build) 
>>
>>
>>
>>
>>
>> On Wed, Dec 30, 2020 at 3:30 PM 'jambodev' via sage-devel 
>>  wrote: 
>> > 
>> > Hi Matthias, all, 
>> > 
>> > As suggested on the other thread, I tried installing the current beta. 
>> But it fails for some reason. Please find my logs attached. 
>> > 
>> > 
>> > -- 
>> > You received this message because you are subscribed to the Google 
>> Groups "sage-devel" group. 
>> > To unsubscribe from this group and stop receiving emails from it, send 
>> an email to sage-devel+...@googlegroups.com. 
>> > To view this discussion on the web visit 
>> https://groups.google.com/d/msgid/sage-devel/417937e4-9235-4b1a-b1fb-7705bbbc5a6cn%40googlegroups.com.
>>  
>>
>>
>

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Re: [sage-devel] build error, building current beta on ubuntu

['jambodev' via sage-devel]

Thanks Dima,

I'll remove that and will retry.

cheers,


On Wednesday, 30 December 2020 at 16:16:18 UTC dim...@gmail.com wrote:

> in the install.log, one sees
>
> [sagelib-9.3.beta4] /usr/local/include/flint/fmpz_poly_mat.h:105:44:
> error: unknown type name ‘flint_bitcnt_t’; did you mean
> ‘flint_rand_t’?
> [sagelib-9.3.beta4] 105 | slong len,
> flint_bitcnt_t bits);
> [sagelib-9.3.beta4] |
> ^~
> [sagelib-9.3.beta4] |
> flint_rand_t
> [sagelib-9.3.beta4] /usr/local/include/flint/fmpz_poly_mat.h:108:41:
> error: unknown type name ‘flint_bitcnt_t’; did you mean
> ‘flint_rand_t’?
> [sagelib-9.3.beta4] 108 | slong len,
> flint_bitcnt_t bits);
>
> which indicates that you most probably have a conflicting copy of
> flint in /usr/local/
> - as well as a copy of a system package flint in /usr/
> (and they are mixed up in the build)
>
>
>
>
>
> On Wed, Dec 30, 2020 at 3:30 PM 'jambodev' via sage-devel
>  wrote:
> >
> > Hi Matthias, all,
> >
> > As suggested on the other thread, I tried installing the current beta. 
> But it fails for some reason. Please find my logs attached.
> >
> >
> > --
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group.
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-devel+...@googlegroups.com.
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> https://groups.google.com/d/msgid/sage-devel/417937e4-9235-4b1a-b1fb-7705bbbc5a6cn%40googlegroups.com
> .
>

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Re: [sage-devel] build error, building current beta on ubuntu

[Dima Pasechnik]

in the install.log, one sees

[sagelib-9.3.beta4] /usr/local/include/flint/fmpz_poly_mat.h:105:44:
error: unknown type name ‘flint_bitcnt_t’; did you mean
‘flint_rand_t’?
[sagelib-9.3.beta4]   105 | slong len,
flint_bitcnt_t bits);
[sagelib-9.3.beta4]   |
^~
[sagelib-9.3.beta4]   |
flint_rand_t
[sagelib-9.3.beta4] /usr/local/include/flint/fmpz_poly_mat.h:108:41:
error: unknown type name ‘flint_bitcnt_t’; did you mean
‘flint_rand_t’?
[sagelib-9.3.beta4]   108 |  slong len,
flint_bitcnt_t bits);

which indicates that you most probably have a conflicting copy of
flint in /usr/local/
- as well as a copy of a system package flint in /usr/
(and they are mixed up in the build)





On Wed, Dec 30, 2020 at 3:30 PM 'jambodev' via sage-devel
 wrote:
>
> Hi Matthias, all,
>
> As suggested on the other thread, I tried installing the current beta. But it 
> fails for some reason. Please find my logs attached.
>
>
> --
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Re: [sage-devel] build error on Mac OS X 10.12.6

[Brian Ball]

Thanks!  That was the clue I needed.  I had a *lot* of "zombie" processes I
needed to kill.

I finished the install:

This looks like the first time you are running Sage.

Cleaning up, do not interrupt this.

Done cleaning.

┌┐

│ SageMath version 8.7, Release Date: 2019-03-23 │

│ Using Python 3.6.6. Type "help()" for help.│

└┘

sage:

On Thu, May 30, 2019 at 7:21 AM Dima Pasechnik  wrote:

> this looks like:
>
> https://lists.apple.com/archives/xcode-users/2012/Nov/msg00215.html
>
> On Thu, 30 May 2019 03:51 Brian Ball,  wrote:
>
>> I am attempting to build Sage from source with Python 3.7.3
>>
>> Logs attached.
>>
>> I run
>>
>> ./configure --with-python=3
>>
>>
>> and at the end I get the following:
>>
>> make[3]: ***
>> [/MyFiles/Numbthy/sage-8.7/local/var/lib/sage/installed/openblas-0.3.5.p0]
>> Error 1
>>
>> make[2]: *** [all-build] Error 2
>>
>>
>> real 74m3.592s
>>
>> user 22m42.854s
>>
>> sys 4m29.081s
>>
>> ***
>>
>> Error building Sage.
>>
>>
>> The following package(s) may have failed to build (not necessarily
>>
>> during this run of 'make all-build'):
>>
>>
>> * package: openblas-0.3.5.p0
>>
>>   log file: /MyFiles/Numbthy/sage-8.7/logs/pkgs/openblas-0.3.5.p0.log
>>
>>   build directory:
>> /MyFiles/Numbthy/sage-8.7/local/var/tmp/sage/build/openblas-0.3.5.p0
>>
>>
>> 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[1]: *** [all-build] Error 1
>>
>> make: *** [build] Error 2
>>
>>
>> Thanks for your help
>>
>>
>> Brian Ball
>>
>>
>> --
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>> 
>> .
>> For more options, visit https://groups.google.com/d/optout.
>>
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Re: [sage-devel] build error on Mac OS X 10.12.6

[Dima Pasechnik]

this looks like:

https://lists.apple.com/archives/xcode-users/2012/Nov/msg00215.html

On Thu, 30 May 2019 03:51 Brian Ball,  wrote:

> I am attempting to build Sage from source with Python 3.7.3
>
> Logs attached.
>
> I run
>
> ./configure --with-python=3
>
>
> and at the end I get the following:
>
> make[3]: ***
> [/MyFiles/Numbthy/sage-8.7/local/var/lib/sage/installed/openblas-0.3.5.p0]
> Error 1
>
> make[2]: *** [all-build] Error 2
>
>
> real 74m3.592s
>
> user 22m42.854s
>
> sys 4m29.081s
>
> ***
>
> Error building Sage.
>
>
> The following package(s) may have failed to build (not necessarily
>
> during this run of 'make all-build'):
>
>
> * package: openblas-0.3.5.p0
>
>   log file: /MyFiles/Numbthy/sage-8.7/logs/pkgs/openblas-0.3.5.p0.log
>
>   build directory:
> /MyFiles/Numbthy/sage-8.7/local/var/tmp/sage/build/openblas-0.3.5.p0
>
>
> 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[1]: *** [all-build] Error 1
>
> make: *** [build] Error 2
>
>
> Thanks for your help
>
>
> Brian Ball
>
>
> --
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Re: [sage-devel] Build error

[Dima Pasechnik]

On Tue, Jan 22, 2019 at 12:53 PM Devika Sugathan <
devikasugathan...@gmail.com> wrote:

>
> Please find the markupsafe-1.0.log file attached.
>

Thanks - if you look into what's in the file you will see a failure to
download the package source.
Try  running make again, making sure your machine is online

>
>
>
> On Mon, Jan 21, 2019 at 11:33 PM Dima Pasechnik  wrote:
>
>> Well, post the log file then: it's
>> /home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log
>>
>>
>> On Mon, Jan 21, 2019 at 5:43 PM Devika Sugathan <
>> devikasugathan...@gmail.com> wrote:
>>
>>> I tried to rebuild it got a new error with some other package.
>>> Error:
>>>
>>> Error building Sage.
>>>
>>> The following package(s) may have failed to build (not necessarily
>>> during this run of 'make all-start'):
>>>
>>> * package: markupsafe-1.0
>>>   log file: /home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log
>>>   build directory:
>>> /home/devikasugathan/sage/local/var/tmp/sage/build/markupsafe-1.0
>>>
>>> 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.
>>>
>>> Makefile:31: recipe for target 'all-start' failed
>>> make[1]: *** [all-start] Error 1
>>> make[1]: Leaving directory '/home/devikasugathan/sage'
>>> Makefile:13: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>>
>>>
>>> On Mon, Jan 21, 2019 at 10:41 PM E. Madison Bray 
>>> wrote:
>>>
 FWIW this is another report (the second I've seen in a week) of
 https://trac.sagemath.org/ticket/26996 which has a potential fix
 awaiting review: https://trac.sagemath.org/ticket/27016

 The issue only occurs when trying to install the gfortran SPKG on Linux
 systems (which is usually unnecessary since most Linux distributions
 already have a perfectly usable gfortran either already installed, or
 available as a standard system package which can be installed).

 On Sun, Jan 20, 2019 at 10:59 AM Devika Sugathan <
 devikasugathan...@gmail.com> wrote:

> Hello,
> I'm a second year engineering student and would like to contribute to
> sage math. Can someone please help me with my doubts on how to proceed and
> please do give me an idea of the skill sets required for contributing. I
> have faced an issue while building the environment.
>
> While running the command *make* I got an error and the screenshot is
> attached below. Later I tried opening the log file gfortran-7.2.0.log and
> received some other error message. Kindly view the screenshots and help me
> out in this regard.
>
>
> --
> Regards
> Devika Sugathan
>
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>>>
>>>
>>> --
>>> Regards
>>> Devika S
>>> FOSS@Amrita 
>>> GitHub  | CodeChef
>>> 
>>>
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Re: [sage-devel] Build error

[Jean-Florent Raymond]

Hello,

Were your computer connected to internet when you tried to build?
If not then try again with internet.
According to the log a problem occurred when trying to download files.




On 22.01.19 13:53, Devika Sugathan wrote:
> Please find the markupsafe-1.0.log file attached.
> 
> 
> 
> On Mon, Jan 21, 2019 at 11:33 PM Dima Pasechnik  wrote:
> 
>> Well, post the log file then: it's
>> /home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log
>>
>>
>> On Mon, Jan 21, 2019 at 5:43 PM Devika Sugathan <
>> devikasugathan...@gmail.com> wrote:
>>
>>> I tried to rebuild it got a new error with some other package.
>>> Error:
>>>
>>> Error building Sage.
>>>
>>> The following package(s) may have failed to build (not necessarily
>>> during this run of 'make all-start'):
>>>
>>> * package: markupsafe-1.0
>>>   log file: /home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log
>>>   build directory:
>>> /home/devikasugathan/sage/local/var/tmp/sage/build/markupsafe-1.0
>>>
>>> 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.
>>>
>>> Makefile:31: recipe for target 'all-start' failed
>>> make[1]: *** [all-start] Error 1
>>> make[1]: Leaving directory '/home/devikasugathan/sage'
>>> Makefile:13: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>>
>>>
>>> On Mon, Jan 21, 2019 at 10:41 PM E. Madison Bray 
>>> wrote:
>>>
 FWIW this is another report (the second I've seen in a week) of
 https://trac.sagemath.org/ticket/26996 which has a potential fix
 awaiting review: https://trac.sagemath.org/ticket/27016

 The issue only occurs when trying to install the gfortran SPKG on Linux
 systems (which is usually unnecessary since most Linux distributions
 already have a perfectly usable gfortran either already installed, or
 available as a standard system package which can be installed).

 On Sun, Jan 20, 2019 at 10:59 AM Devika Sugathan <
 devikasugathan...@gmail.com> wrote:

> Hello,
> I'm a second year engineering student and would like to contribute to
> sage math. Can someone please help me with my doubts on how to proceed and
> please do give me an idea of the skill sets required for contributing. I
> have faced an issue while building the environment.
>
> While running the command *make* I got an error and the screenshot is
> attached below. Later I tried opening the log file gfortran-7.2.0.log and
> received some other error message. Kindly view the screenshots and help me
> out in this regard.
>
>
> --
> Regards
> Devika Sugathan
>
> --
> You received this message because you are subscribed to the Google
> Groups "sage-devel" group.
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> an email to sage-devel+unsubscr...@googlegroups.com.
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>>>
>>>
>>> --
>>> Regards
>>> Devika S
>>> FOSS@Amrita 
>>> GitHub  | CodeChef
>>> 
>>>
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>>>
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Re: [sage-devel] Build error

[Devika Sugathan]

Please find the markupsafe-1.0.log file attached.



On Mon, Jan 21, 2019 at 11:33 PM Dima Pasechnik  wrote:

> Well, post the log file then: it's
> /home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log
>
>
> On Mon, Jan 21, 2019 at 5:43 PM Devika Sugathan <
> devikasugathan...@gmail.com> wrote:
>
>> I tried to rebuild it got a new error with some other package.
>> Error:
>>
>> Error building Sage.
>>
>> The following package(s) may have failed to build (not necessarily
>> during this run of 'make all-start'):
>>
>> * package: markupsafe-1.0
>>   log file: /home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log
>>   build directory:
>> /home/devikasugathan/sage/local/var/tmp/sage/build/markupsafe-1.0
>>
>> 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.
>>
>> Makefile:31: recipe for target 'all-start' failed
>> make[1]: *** [all-start] Error 1
>> make[1]: Leaving directory '/home/devikasugathan/sage'
>> Makefile:13: recipe for target 'all' failed
>> make: *** [all] Error 2
>>
>>
>> On Mon, Jan 21, 2019 at 10:41 PM E. Madison Bray 
>> wrote:
>>
>>> FWIW this is another report (the second I've seen in a week) of
>>> https://trac.sagemath.org/ticket/26996 which has a potential fix
>>> awaiting review: https://trac.sagemath.org/ticket/27016
>>>
>>> The issue only occurs when trying to install the gfortran SPKG on Linux
>>> systems (which is usually unnecessary since most Linux distributions
>>> already have a perfectly usable gfortran either already installed, or
>>> available as a standard system package which can be installed).
>>>
>>> On Sun, Jan 20, 2019 at 10:59 AM Devika Sugathan <
>>> devikasugathan...@gmail.com> wrote:
>>>
 Hello,
 I'm a second year engineering student and would like to contribute to
 sage math. Can someone please help me with my doubts on how to proceed and
 please do give me an idea of the skill sets required for contributing. I
 have faced an issue while building the environment.

 While running the command *make* I got an error and the screenshot is
 attached below. Later I tried opening the log file gfortran-7.2.0.log and
 received some other error message. Kindly view the screenshots and help me
 out in this regard.


 --
 Regards
 Devika Sugathan

 --
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>>> --
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>>>
>>
>>
>> --
>> Regards
>> Devika S
>> FOSS@Amrita 
>> GitHub  | CodeChef
>> 
>>
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FOSS@Amrita 
GitHub  | CodeChef


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Re: [sage-devel] Build error

[Dima Pasechnik]

Well, post the log file then: it's
/home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log


On Mon, Jan 21, 2019 at 5:43 PM Devika Sugathan 
wrote:

> I tried to rebuild it got a new error with some other package.
> Error:
>
> Error building Sage.
>
> The following package(s) may have failed to build (not necessarily
> during this run of 'make all-start'):
>
> * package: markupsafe-1.0
>   log file: /home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log
>   build directory:
> /home/devikasugathan/sage/local/var/tmp/sage/build/markupsafe-1.0
>
> 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.
>
> Makefile:31: recipe for target 'all-start' failed
> make[1]: *** [all-start] Error 1
> make[1]: Leaving directory '/home/devikasugathan/sage'
> Makefile:13: recipe for target 'all' failed
> make: *** [all] Error 2
>
>
> On Mon, Jan 21, 2019 at 10:41 PM E. Madison Bray 
> wrote:
>
>> FWIW this is another report (the second I've seen in a week) of
>> https://trac.sagemath.org/ticket/26996 which has a potential fix
>> awaiting review: https://trac.sagemath.org/ticket/27016
>>
>> The issue only occurs when trying to install the gfortran SPKG on Linux
>> systems (which is usually unnecessary since most Linux distributions
>> already have a perfectly usable gfortran either already installed, or
>> available as a standard system package which can be installed).
>>
>> On Sun, Jan 20, 2019 at 10:59 AM Devika Sugathan <
>> devikasugathan...@gmail.com> wrote:
>>
>>> Hello,
>>> I'm a second year engineering student and would like to contribute to
>>> sage math. Can someone please help me with my doubts on how to proceed and
>>> please do give me an idea of the skill sets required for contributing. I
>>> have faced an issue while building the environment.
>>>
>>> While running the command *make* I got an error and the screenshot is
>>> attached below. Later I tried opening the log file gfortran-7.2.0.log and
>>> received some other error message. Kindly view the screenshots and help me
>>> out in this regard.
>>>
>>>
>>> --
>>> Regards
>>> Devika Sugathan
>>>
>>> --
>>> You received this message because you are subscribed to the Google
>>> Groups "sage-devel" group.
>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to sage-devel+unsubscr...@googlegroups.com.
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>>> For more options, visit https://groups.google.com/d/optout.
>>>
>> --
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>>
>
>
> --
> Regards
> Devika S
> FOSS@Amrita 
> GitHub  | CodeChef
> 
>
> --
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Re: [sage-devel] Build error

[Devika Sugathan]

I tried to rebuild it got a new error with some other package.
Error:

Error building Sage.

The following package(s) may have failed to build (not necessarily
during this run of 'make all-start'):

* package: markupsafe-1.0
  log file: /home/devikasugathan/sage/logs/pkgs/markupsafe-1.0.log
  build directory:
/home/devikasugathan/sage/local/var/tmp/sage/build/markupsafe-1.0

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.

Makefile:31: recipe for target 'all-start' failed
make[1]: *** [all-start] Error 1
make[1]: Leaving directory '/home/devikasugathan/sage'
Makefile:13: recipe for target 'all' failed
make: *** [all] Error 2


On Mon, Jan 21, 2019 at 10:41 PM E. Madison Bray 
wrote:

> FWIW this is another report (the second I've seen in a week) of
> https://trac.sagemath.org/ticket/26996 which has a potential fix awaiting
> review: https://trac.sagemath.org/ticket/27016
>
> The issue only occurs when trying to install the gfortran SPKG on Linux
> systems (which is usually unnecessary since most Linux distributions
> already have a perfectly usable gfortran either already installed, or
> available as a standard system package which can be installed).
>
> On Sun, Jan 20, 2019 at 10:59 AM Devika Sugathan <
> devikasugathan...@gmail.com> wrote:
>
>> Hello,
>> I'm a second year engineering student and would like to contribute to
>> sage math. Can someone please help me with my doubts on how to proceed and
>> please do give me an idea of the skill sets required for contributing. I
>> have faced an issue while building the environment.
>>
>> While running the command *make* I got an error and the screenshot is
>> attached below. Later I tried opening the log file gfortran-7.2.0.log and
>> received some other error message. Kindly view the screenshots and help me
>> out in this regard.
>>
>>
>> --
>> Regards
>> Devika Sugathan
>>
>> --
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>> "sage-devel" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to sage-devel+unsubscr...@googlegroups.com.
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>>
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-- 
Regards
Devika S
FOSS@Amrita 
GitHub  | CodeChef


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Re: [sage-devel] Build error

[E. Madison Bray]

FWIW this is another report (the second I've seen in a week) of
https://trac.sagemath.org/ticket/26996 which has a potential fix awaiting
review: https://trac.sagemath.org/ticket/27016

The issue only occurs when trying to install the gfortran SPKG on Linux
systems (which is usually unnecessary since most Linux distributions
already have a perfectly usable gfortran either already installed, or
available as a standard system package which can be installed).

On Sun, Jan 20, 2019 at 10:59 AM Devika Sugathan <
devikasugathan...@gmail.com> wrote:

> Hello,
> I'm a second year engineering student and would like to contribute to sage
> math. Can someone please help me with my doubts on how to proceed and
> please do give me an idea of the skill sets required for contributing. I
> have faced an issue while building the environment.
>
> While running the command *make* I got an error and the screenshot is
> attached below. Later I tried opening the log file gfortran-7.2.0.log and
> received some other error message. Kindly view the screenshots and help me
> out in this regard.
>
>
> --
> Regards
> Devika Sugathan
>
> --
> You received this message because you are subscribed to the Google Groups
> "sage-devel" group.
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> email to sage-devel+unsubscr...@googlegroups.com.
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>

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Re: [sage-devel] Build error

[Jeroen Demeyer]

The error message seems to imply that you tried to install (part of) 
Sage as a different user. Maybe the safest option is to delete your 
installation completely:


rm -rf /home/devikasugathan/sage

and then try again.

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Re: [sage-devel] Build error

[Jan Groenewald]

Hi

On Sun, 20 Jan 2019 at 12:25, Dima Pasechnik  wrote:

>
> E.g. on a debian system you'd do
>
> sudo apt-get install binutils gcc g++ gfortran make m4 perl tar \git openssl 
> libssl-dev
>
> (I think it's actually outdated, you should add yasm,
> libcurl4-openssl-dev, lzma-dev, xz to this list of packages)
>

xz-utils instead of xz?

Regards,
Jan

-- 
  .~.
  /V\ Jan Groenewald
 /( )\www.aims.ac.za
 ^^-^^

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Re: [sage-devel] Build error

[Eric Gourgoulhon]

Le dimanche 20 janvier 2019 11:25:36 UTC+1, Dima Pasechnik a écrit :
>
>
> First of all, on a Linux system you almost never would need to build 
> Sage-supplied gfortran, it's much easier to install a system-wide gfortran 
> using the system's package manager.
> See 
> http://doc.sagemath.org/html/en/installation/source.html#installing-prerequisites
>
> E.g. on a debian system you'd do
>
> sudo apt-get install binutils gcc g++ gfortran make m4 perl tar \git openssl 
> libssl-dev
>
> (I think it's actually outdated, you should add yasm, 
> libcurl4-openssl-dev, lzma-dev, xz to this list of packages)
>
>
For Ubuntu 18.04, a list of required system packages to build Sage is 
available at
https://wiki.sagemath.org/prerequisitesUbuntu

Eric.

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Re: [sage-devel] Build error

[Dima Pasechnik]

Dear Devika,

On Sun, Jan 20, 2019 at 9:59 AM Devika Sugathan 
wrote:

> Hello,
> I'm a second year engineering student and would like to contribute to sage
> math. Can someone please help me with my doubts on how to proceed and
> please do give me an idea of the skill sets required for contributing. I
> have faced an issue while building the environment.
>
> While running the command *make* I got an error and the screenshot is
> attached below. Later I tried opening the log file gfortran-7.2.0.log and
> received some other error message. Kindly view the screenshots and help me
> out in this regard.
>

First of all, on a Linux system you almost never would need to build
Sage-supplied gfortran, it's much easier to install a system-wide gfortran
using the system's package manager.
See
http://doc.sagemath.org/html/en/installation/source.html#installing-prerequisites

E.g. on a debian system you'd do

sudo apt-get install binutils gcc g++ gfortran make m4 perl tar \git
openssl libssl-dev

(I think it's actually outdated, you should add yasm, libcurl4-openssl-dev,
lzma-dev, xz to this list of packages)

Then, you are using zsh, I am not sure it's well-supported by Sage. Could
you build Sage using bash?


>
>
> --
> Regards
> Devika Sugathan
>
> --
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>

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Re: [sage-devel] Build error

[David . Coudert]

I tried some of the suggestions:
1) deleting SAGE_LOCAL/lib/libpython* and then make -> failed
2) make distclean && make build -> success

I still have to add the optional packages I need, but it's working.

Thanks.
David.

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Re: [sage-devel] Build error

[Dima Pasechnik]

yeah, I agree that a stale library is the most probable reason for this error.

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Re: [sage-devel] Build error

[François Bissey]

OK this looks suspiciously like 
https://bugs.python.org/issue30074
which was fixed by 
https://github.com/python/cpython/pull/1154
which should be in 2.7.14.
What I suspect is happening is that those failures happen when
people upgrade python from 2.7.13 (or older) to 2.7.14.
I have a feeling that when the extension (and there is more than one failing)
is loaded to be tested as being successfully built, the wrong libpython is 
loaded.
Because of our use of rpath, libpython from python 2.7.13 is used and missing 
that particular symbol.
If this is really the case, deleting SAGE_LOCAL/lib/libpython* should be enough
to fix the issue.

François

> On 8/12/2017, at 09:17, Dima Pasechnik  wrote:
> 
> it would be interesting that try to debug this.
> You most probably can get a working version by doing
> 
> make distclean
> 
> (making sure it succeeds!)
> and then building,
> so please do 
> 
> cp -a 
> 
> of the whole tree before doing this...
> 
> 
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Re: [sage-devel] Build error

[Dima Pasechnik]

it would be interesting that try to debug this.
You most probably can get a working version by doing

make distclean

(making sure it succeeds!)
and then building,
so please do 

cp -a 

of the whole tree before doing this...


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Re: [sage-devel] Build error

[Jeroen Demeyer]

On 2017-12-07 15:13, Simon King wrote:

How to fix that?


This is a bug that several people have reported but I don't know how to 
reproduce it.



make distclean and start again?


That works.

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[sage-devel] Build error

[Simon King]

Hi!

On a laptop that I haven't used for a while, I tried to upgrade Sage.
I.e., I did "git checkout develop", "git pull" and "make".

While building python2-2.7.15.p2, I get
  [python2-2.7.14.p2] ImportError: No module named _ctypes
  [python2-2.7.14.p2] ctypes module failed to import

and

  [python2-2.7.14.p2] Python build finished, but the necessary bits to
  build these modules were not found:
  [python2-2.7.14.p2] _bsddb _tkinter   bsddb185
  [python2-2.7.14.p2] dbmdl gdbm
  [python2-2.7.14.p2] imageopsunaudiodev
  [python2-2.7.14.p2] To find the necessary bits, look in setup.py in
  detect_modules() for the module's name.
  [python2-2.7.14.p2] 
  [python2-2.7.14.p2] 
  [python2-2.7.14.p2] Failed to build these modules:
  [python2-2.7.14.p2] _ctypes_elementtree
  _multiprocessing
  [python2-2.7.14.p2] array  mmap   

How to fix that? make distclean and start again?

Best regards,
Simon


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[sage-devel] Build Error for 7.3 beta 3 on Mac OS X 10.11.5

[paulmasson]

You need to perform an explicit installation of the Xcode command line tools. I 
had the same error recently and that solved it.

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Re: [sage-devel] Build Error for 7.3 beta 3 on Mac OS X 10.11.5

[Francois Bissey]

Not really without some logs. But I guess I’ll try locally at some point…
when I have dealt with other problems...

François

> On 8/06/2016, at 10:33, Rebecca Miller  wrote:
> 
> Any thoughts on how to get around this?
> 

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[sage-devel] Build Error for 7.3 beta 3 on Mac OS X 10.11.5

[Rebecca Miller]

I'm having trouble building the newest beta. 
I have updated my OS X and XCode to the latest version.
I have  make distclean.
The error I'm getting is " Error installing package gcc-4.9.3.p1".

Any thoughts on how to get around this?

Thanks,

Rebecca M

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Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[Francois Bissey]

I have personally mostly eliminated the use of LD_LIBRARY_PATH from my linux 
cluster
in favour of coding runpath in programs and libraries so that it is never an 
issue (the only 
exception would be openfoam I think).
In the case of gcc, it means changing the specs (as in gcc -dumpspecs) to 
enforce its own 
runpath at compile time. You have to patch gcc sources to achieve this but I 
recommend it. 
The only case where it doesn’t work is when ld is called directly rather than 
through the compiler.

François

> On 14/01/2015, at 06:16, crooksc...@gmail.com wrote:
> 
> Thank you.  I had forgotten to include the gcc "lib64" directory in my 
> LD_LIBRARY_PATH.  I have updated the appropriate module file.  I will see 
> what happens next.
> 
> Cindy
> 
> On Monday, January 12, 2015 at 5:59:51 PM UTC-6, François wrote:
> It looks like something has gone wrong with LD_LIBRARY_PATH & co. This means 
> that libstdc++ found when running sage is from older version of gcc than the 
> one used 
> to compile sage. Here you find libstdc++ from the system (gcc-4.3.4 I 
> presume) rather 
> than whatever you used to compile. 
> I assume you have a build environment that is different from the system one 
> (I have at 
> least 5 on the local power7 cluster). 
> 
> François 
> > On 13/01/2015, at 11:21, crook...@gmail.com wrote: 
> > 
> > Setting the effective group to the same as the group on the build directory 
> > did allow pynac to compile.  I am now stuck on an error in 
> > conway_polynomials-0.4.p0. 
> > 
> > ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found 
> > (required by 
> > /hpc/tstapps/src/sage/sage-6.4.1/local/lib/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
> >  
> > 
> > I have not had a chance to investigate, yet.  It may be a couple of days 
> > before I can get back to this. 
> > 
> > Cindy 
> > 
> > 
> > On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com wrote: 
> > I am trying to compile sage-6.4.1 for one of my users.  I am working on a 
> > SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my 
> > personal account and I own the build directory and all of the 
> > directories/files for gcc and python.  I am still getting the following 
> > error: 
> > 
> > checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not 
> > adding 
> >  directory '' to sys.path since it's writable by an untrusted group. 
> > Untrusted users could put files in this directory which might then be 
> > imported b 
> > y your Python code. As a general precaution from similar exploits, you 
> > should no 
> > t execute Python code from this directory 
> > 
> > I have attached the sage_pynac-0.3.2.log for you to review.  I have tried 
> > looking through previous posts, but I don't see anything that quite matches 
> > this situation. 
> > 
> > Thanks in advance for your help. 
> > 
> > Cindy 
> > 
> > On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com wrote: 
> > I am trying to compile sage-6.4.1 for one of my users.  I am working on a 
> > SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my 
> > personal account and I own the build directory and all of the 
> > directories/files for gcc and python.  I am still getting the following 
> > error: 
> > 
> > checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not 
> > adding 
> >  directory '' to sys.path since it's writable by an untrusted group. 
> > Untrusted users could put files in this directory which might then be 
> > imported b 
> > y your Python code. As a general precaution from similar exploits, you 
> > should no 
> > t execute Python code from this directory 
> > 
> > I have attached the sage_pynac-0.3.2.log for you to review.  I have tried 
> > looking through previous posts, but I don't see anything that quite matches 
> > this situation. 
> > 
> > Thanks in advance for your help. 
> > 
> > Cindy 
> > 
> > -- 
> > You received this message because you are subscribed to the Google Groups 
> > "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send an 
> > email to sage-devel+...@googlegroups.com. 
> > To post to this group, send email to sage-...@googlegroups.com. 
> > Visit this group at http://groups.google.com/group/sage-devel. 
> > For more options, visit https://groups.google.com/d/optout. 
> 
> 
> On Monday, January 12, 2015 at 5:59:51 PM UTC-6, François wrote:
> It looks like something has gone wrong with LD_LIBRARY_PATH & co. This means 
> that libstdc++ found when running sage is from older version of gcc than the 
> one used 
> to compile sage. Here you find libstdc++ from the system (gcc-4.3.4 I 
> presume) rather 
> than whatever you used to compile. 
> I assume you have a build environment that is different from the system one 
> (I have at 
> least 5 on the local power7 cluster). 
> 
> François 
> > On 13/01/2015, at 11:21, crook...@gmail.com wrote: 
> > 
> > Setting the e

Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[crookscj02]

The compile completed.  I have installed it in the "official" location.  I 
will now ask the user  to  run it through its paces.

Thanks for your help

Cindy

On Tuesday, January 13, 2015 at 11:16:29 AM UTC-6, crook...@gmail.com wrote:
>
> Thank you.  I had forgotten to include the gcc "lib64" directory in my 
> LD_LIBRARY_PATH.  I have updated the appropriate module file.  I will see 
> what happens next.
>
> Cindy
>
> On Monday, January 12, 2015 at 5:59:51 PM UTC-6, François wrote:
>>
>> It looks like something has gone wrong with LD_LIBRARY_PATH & co. This 
>> means 
>> that libstdc++ found when running sage is from older version of gcc than 
>> the one used 
>> to compile sage. Here you find libstdc++ from the system (gcc-4.3.4 I 
>> presume) rather 
>> than whatever you used to compile. 
>> I assume you have a build environment that is different from the system 
>> one (I have at 
>> least 5 on the local power7 cluster). 
>>
>> François 
>> > On 13/01/2015, at 11:21, crook...@gmail.com wrote: 
>> > 
>> > Setting the effective group to the same as the group on the build 
>> directory did allow pynac to compile.  I am now stuck on an error in 
>> > conway_polynomials-0.4.p0. 
>> > 
>> > ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not 
>> found (required by 
>> /hpc/tstapps/src/sage/sage-6.4.1/local/lib/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
>>  
>>
>> > 
>> > I have not had a chance to investigate, yet.  It may be a couple of 
>> days before I can get back to this. 
>> > 
>> > Cindy 
>> > 
>> > 
>> > On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com 
>> wrote: 
>> > I am trying to compile sage-6.4.1 for one of my users.  I am working on 
>> a SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my 
>> personal account and I own the build directory and all of the 
>> directories/files for gcc and python.  I am still getting the following 
>> error: 
>> > 
>> > checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: 
>> not adding 
>> >  directory '' to sys.path since it's writable by an untrusted group. 
>> > Untrusted users could put files in this directory which might then be 
>> imported b 
>> > y your Python code. As a general precaution from similar exploits, you 
>> should no 
>> > t execute Python code from this directory 
>> > 
>> > I have attached the sage_pynac-0.3.2.log for you to review.  I have 
>> tried looking through previous posts, but I don't see anything that quite 
>> matches this situation. 
>> > 
>> > Thanks in advance for your help. 
>> > 
>> > Cindy 
>> > 
>> > On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com 
>> wrote: 
>> > I am trying to compile sage-6.4.1 for one of my users.  I am working on 
>> a SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my 
>> personal account and I own the build directory and all of the 
>> directories/files for gcc and python.  I am still getting the following 
>> error: 
>> > 
>> > checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: 
>> not adding 
>> >  directory '' to sys.path since it's writable by an untrusted group. 
>> > Untrusted users could put files in this directory which might then be 
>> imported b 
>> > y your Python code. As a general precaution from similar exploits, you 
>> should no 
>> > t execute Python code from this directory 
>> > 
>> > I have attached the sage_pynac-0.3.2.log for you to review.  I have 
>> tried looking through previous posts, but I don't see anything that quite 
>> matches this situation. 
>> > 
>> > Thanks in advance for your help. 
>> > 
>> > Cindy 
>> > 
>> > -- 
>> > You received this message because you are subscribed to the Google 
>> Groups "sage-devel" group. 
>> > To unsubscribe from this group and stop receiving emails from it, send 
>> an email to sage-devel+...@googlegroups.com. 
>> > To post to this group, send email to sage-...@googlegroups.com. 
>> > Visit this group at http://groups.google.com/group/sage-devel. 
>> > For more options, visit https://groups.google.com/d/optout. 
>>
>>
> On Monday, January 12, 2015 at 5:59:51 PM UTC-6, François wrote:
>>
>> It looks like something has gone wrong with LD_LIBRARY_PATH & co. This 
>> means 
>> that libstdc++ found when running sage is from older version of gcc than 
>> the one used 
>> to compile sage. Here you find libstdc++ from the system (gcc-4.3.4 I 
>> presume) rather 
>> than whatever you used to compile. 
>> I assume you have a build environment that is different from the system 
>> one (I have at 
>> least 5 on the local power7 cluster). 
>>
>> François 
>> > On 13/01/2015, at 11:21, crook...@gmail.com wrote: 
>> > 
>> > Setting the effective group to the same as the group on the build 
>> directory did allow pynac to compile.  I am now stuck on an error in 
>> > conway_polynomials-0.4.p0. 
>> > 
>> > ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not 
>> found (required by 
>> 

Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[crookscj02]

Thank you.  I had forgotten to include the gcc "lib64" directory in my 
LD_LIBRARY_PATH.  I have updated the appropriate module file.  I will see 
what happens next.

Cindy

On Monday, January 12, 2015 at 5:59:51 PM UTC-6, François wrote:
>
> It looks like something has gone wrong with LD_LIBRARY_PATH & co. This 
> means 
> that libstdc++ found when running sage is from older version of gcc than 
> the one used 
> to compile sage. Here you find libstdc++ from the system (gcc-4.3.4 I 
> presume) rather 
> than whatever you used to compile. 
> I assume you have a build environment that is different from the system 
> one (I have at 
> least 5 on the local power7 cluster). 
>
> François 
> > On 13/01/2015, at 11:21, crook...@gmail.com  wrote: 
> > 
> > Setting the effective group to the same as the group on the build 
> directory did allow pynac to compile.  I am now stuck on an error in 
> > conway_polynomials-0.4.p0. 
> > 
> > ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not 
> found (required by 
> /hpc/tstapps/src/sage/sage-6.4.1/local/lib/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
>  
>
> > 
> > I have not had a chance to investigate, yet.  It may be a couple of days 
> before I can get back to this. 
> > 
> > Cindy 
> > 
> > 
> > On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com 
> wrote: 
> > I am trying to compile sage-6.4.1 for one of my users.  I am working on 
> a SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my 
> personal account and I own the build directory and all of the 
> directories/files for gcc and python.  I am still getting the following 
> error: 
> > 
> > checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: 
> not adding 
> >  directory '' to sys.path since it's writable by an untrusted group. 
> > Untrusted users could put files in this directory which might then be 
> imported b 
> > y your Python code. As a general precaution from similar exploits, you 
> should no 
> > t execute Python code from this directory 
> > 
> > I have attached the sage_pynac-0.3.2.log for you to review.  I have 
> tried looking through previous posts, but I don't see anything that quite 
> matches this situation. 
> > 
> > Thanks in advance for your help. 
> > 
> > Cindy 
> > 
> > On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com 
> wrote: 
> > I am trying to compile sage-6.4.1 for one of my users.  I am working on 
> a SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my 
> personal account and I own the build directory and all of the 
> directories/files for gcc and python.  I am still getting the following 
> error: 
> > 
> > checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: 
> not adding 
> >  directory '' to sys.path since it's writable by an untrusted group. 
> > Untrusted users could put files in this directory which might then be 
> imported b 
> > y your Python code. As a general precaution from similar exploits, you 
> should no 
> > t execute Python code from this directory 
> > 
> > I have attached the sage_pynac-0.3.2.log for you to review.  I have 
> tried looking through previous posts, but I don't see anything that quite 
> matches this situation. 
> > 
> > Thanks in advance for your help. 
> > 
> > Cindy 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-devel+...@googlegroups.com . 
> > To post to this group, send email to sage-...@googlegroups.com 
> . 
> > Visit this group at http://groups.google.com/group/sage-devel. 
> > For more options, visit https://groups.google.com/d/optout. 
>
>
On Monday, January 12, 2015 at 5:59:51 PM UTC-6, François wrote:
>
> It looks like something has gone wrong with LD_LIBRARY_PATH & co. This 
> means 
> that libstdc++ found when running sage is from older version of gcc than 
> the one used 
> to compile sage. Here you find libstdc++ from the system (gcc-4.3.4 I 
> presume) rather 
> than whatever you used to compile. 
> I assume you have a build environment that is different from the system 
> one (I have at 
> least 5 on the local power7 cluster). 
>
> François 
> > On 13/01/2015, at 11:21, crook...@gmail.com  wrote: 
> > 
> > Setting the effective group to the same as the group on the build 
> directory did allow pynac to compile.  I am now stuck on an error in 
> > conway_polynomials-0.4.p0. 
> > 
> > ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not 
> found (required by 
> /hpc/tstapps/src/sage/sage-6.4.1/local/lib/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
>  
>
> > 
> > I have not had a chance to investigate, yet.  It may be a couple of days 
> before I can get back to this. 
> > 
> > Cindy 
> > 
> > 
> > On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com 
> wrote: 
> > I am trying to

Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[Francois Bissey]

It looks like something has gone wrong with LD_LIBRARY_PATH & co. This means
that libstdc++ found when running sage is from older version of gcc than the 
one used 
to compile sage. Here you find libstdc++ from the system (gcc-4.3.4 I presume) 
rather
than whatever you used to compile. 
I assume you have a build environment that is different from the system one (I 
have at
least 5 on the local power7 cluster).

François
> On 13/01/2015, at 11:21, crooksc...@gmail.com wrote:
> 
> Setting the effective group to the same as the group on the build directory 
> did allow pynac to compile.  I am now stuck on an error in 
> conway_polynomials-0.4.p0.
> 
> ImportError: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found 
> (required by 
> /hpc/tstapps/src/sage/sage-6.4.1/local/lib/python2.7/site-packages/sage/matrix/matrix_modn_dense_float.so)
> 
> I have not had a chance to investigate, yet.  It may be a couple of days 
> before I can get back to this.
> 
> Cindy
> 
> 
> On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com wrote:
> I am trying to compile sage-6.4.1 for one of my users.  I am working on a 
> SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my personal 
> account and I own the build directory and all of the directories/files for 
> gcc and python.  I am still getting the following error:
> 
> checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not 
> adding
>  directory '' to sys.path since it's writable by an untrusted group.
> Untrusted users could put files in this directory which might then be 
> imported b
> y your Python code. As a general precaution from similar exploits, you should 
> no
> t execute Python code from this directory
> 
> I have attached the sage_pynac-0.3.2.log for you to review.  I have tried 
> looking through previous posts, but I don't see anything that quite matches 
> this situation.
> 
> Thanks in advance for your help.
> 
> Cindy
> 
> On Thursday, January 8, 2015 at 1:43:22 PM UTC-6, crook...@gmail.com wrote:
> I am trying to compile sage-6.4.1 for one of my users.  I am working on a 
> SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my personal 
> account and I own the build directory and all of the directories/files for 
> gcc and python.  I am still getting the following error:
> 
> checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not 
> adding
>  directory '' to sys.path since it's writable by an untrusted group.
> Untrusted users could put files in this directory which might then be 
> imported b
> y your Python code. As a general precaution from similar exploits, you should 
> no
> t execute Python code from this directory
> 
> I have attached the sage_pynac-0.3.2.log for you to review.  I have tried 
> looking through previous posts, but I don't see anything that quite matches 
> this situation.
> 
> Thanks in advance for your help.
> 
> Cindy
> 
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[sage-devel] Build error for sage 6.4 beta 5 under cygwin64

[Sebastien Gouezel]

The webpage http://trac.sagemath.org/wiki/Cygwin64Port indicates that 
sage can now be built under cygwin64 almost out of the box. So, I tried, 
but I failed...


Here are the problems I encountered, maybe someone with better computer 
skills can see what is going on. My sage version is sage 6.4beta5 with 
#17365 pulled. Very recent cygwin64


- First, pyzmq did not compile, because of undefined references in 
libzmq.a. It seems that the flag -no-undefined was not passed to ld 
while building libzmq.a (despite #17333). I hacked the makefile to make 
sure that the flag was passed when compiling zeromq, this solved the issue.


- Then, while compiling sage proper, I get the following error

gcc -I/usr/include/ncurses -fno-strict-aliasing -g -O2 -DNDEBUG -g 
-fwrapv -O3 -Wall -I/home/Sebastien/sage/local/include 
-I/home/Sebastien/sage/local/include/csage -I/home/Sebastien/sage/src 
-I/home/Sebastien/sage/src/sage/ext 
-I/home/Sebastien/sage/local/include/python2.7 -c 
build/cythonized/sage/graphs/distances_all_pairs.c -o 
build/temp.cygwin-1.7.33-x86_64-2.7/build/cythonized/sage/graphs/distances_all_pairs.o 
-fno-strict-aliasing -w -fno-tree-dominator-opts


gcc -shared -Wl,--enable-auto-image-base 
-L/home/Sebastien/sage/local/lib 
build/temp.cygwin-1.7.33-x86_64-2.7/build/cythonized/sage/graphs/distances_all_pairs.o 
-L/home/Sebastien/sage/local/lib 
-L/home/Sebastien/sage/local/lib/python2.7/config 
-L/home/Sebastien/sage/local/lib -lcsage -lpython2.7 -o 
build/lib.cygwin-1.7.33-x86_64-2.7/sage/graphs/distances_all_pairs.dll


build/temp.cygwin-1.7.33-x86_64-2.7/build/cythonized/sage/graphs/distances_all_pairs.o: 
dans la fonction « 
__pyx_f_4sage_6graphs_19distances_all_pairs_bitset_clear »:


/home/Sebastien/sage/src/build/cythonized/sage/graphs/distances_all_pairs.c:2010: 
référence indéfinie vers « __imp___gmpn_zero »


/home/Sebastien/sage/src/build/cythonized/sage/graphs/distances_all_pairs.c:2010:(.text+0x1493): 
relocalisation tronquée pour concorder avec la taille: R_X86_64_PC32 
vers le symbole indéfini __imp___gmpn_zero


/home/Sebastien/sage/src/build/cythonized/sage/graphs/distances_all_pairs.c:2010: 
référence indéfinie vers « __imp___gmpn_zero »


/home/Sebastien/sage/src/build/cythonized/sage/graphs/distances_all_pairs.c:2010:(.text+0xba8e): 
relocalisation tronquée pour concorder avec la taille: R_X86_64_PC32 
vers le symbole indéfini __imp___gmpn_zero


collect2: erreur: ld a retourné 1 code d'état d'exécution

Looks like a problem with mpir, or a linking problem... I can give more 
details or log files if needed.



Sebastien

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Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[crookscj02]

It didn't seem to like just changing the effective group and failed almost 
immediately trying to build gcc.  I have started afresh with hpcapps as the 
effective group and will see how far I can get.

On Thursday, January 8, 2015 at 3:38:28 PM UTC-6, François wrote:
>
> Nothing to do apart from “make”. 
> > On 9/01/2015, at 10:21, crook...@gmail.com  wrote: 
> > 
> > Thank you.  I will give it a try.   
> > 
> > Pardon my ignorance, but is there anything I have to do to pick up the 
> "make" where I left off?  Or, do I need to start from the beginning? 
> > 
> > Cindy 
> > 
> > On Thursday, January 8, 2015 at 2:41:12 PM UTC-6, François wrote: 
> > Not completely sure since the error is about the folder’s group 
> permission but that’s worth a try. 
> > I am not sure how the “security” stuff has been implemented, it may be 
> that the group is outside 
> > a deemed safe range. 
> > Hum, this was implemented here: 
> > 
> https://github.com/sagemath/sage/blob/master/build/pkgs/python/patches/sys_path_security.patch#L251
>  
> > I am guessing in your case the group is writable which of course you 
> want (Fellow HPC admin here). 
> > A strategy would be to build in personal directory and then install. 
> > 
> > François 
> > 
> > > On 9/01/2015, at 09:26, crook...@gmail.com wrote: 
> > > 
> > > 
> > > 
> > > O 
> > > I am part of the root  group.  Below is the list of groups that I am 
> part of: 
> > > 
> > >   gid=255(hpcadmin) 
> groups=255(hpcadmin),254(hpc),702(techgrp),23171(hpcapps),23173(hpctrain),42124(hpc-vasp),44679(hpc-reems),47919(hpc-sys),61860(rsmadmins)
>  
>
> > > 
> > > The directories and software that I have mentioned are owned by the 
> hpcapps group.  Do I need to have that be my "effective" group for the sage 
> python to work? 
> > > 
> > > Cindy 
> > > 
> > > -- 
> > > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> > > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-devel+...@googlegroups.com. 
> > > To post to this group, send email to sage-...@googlegroups.com. 
> > > Visit this group at http://groups.google.com/group/sage-devel. 
> > > For more options, visit https://groups.google.com/d/optout. 
> > 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
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> an email to sage-devel+...@googlegroups.com . 
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> . 
> > Visit this group at http://groups.google.com/group/sage-devel. 
> > For more options, visit https://groups.google.com/d/optout. 
>
>
On Thursday, January 8, 2015 at 3:38:28 PM UTC-6, François wrote:
>
> Nothing to do apart from “make”. 
> > On 9/01/2015, at 10:21, crook...@gmail.com  wrote: 
> > 
> > Thank you.  I will give it a try.   
> > 
> > Pardon my ignorance, but is there anything I have to do to pick up the 
> "make" where I left off?  Or, do I need to start from the beginning? 
> > 
> > Cindy 
> > 
> > On Thursday, January 8, 2015 at 2:41:12 PM UTC-6, François wrote: 
> > Not completely sure since the error is about the folder’s group 
> permission but that’s worth a try. 
> > I am not sure how the “security” stuff has been implemented, it may be 
> that the group is outside 
> > a deemed safe range. 
> > Hum, this was implemented here: 
> > 
> https://github.com/sagemath/sage/blob/master/build/pkgs/python/patches/sys_path_security.patch#L251
>  
> > I am guessing in your case the group is writable which of course you 
> want (Fellow HPC admin here). 
> > A strategy would be to build in personal directory and then install. 
> > 
> > François 
> > 
> > > On 9/01/2015, at 09:26, crook...@gmail.com wrote: 
> > > 
> > > 
> > > 
> > > O 
> > > I am part of the root  group.  Below is the list of groups that I am 
> part of: 
> > > 
> > >   gid=255(hpcadmin) 
> groups=255(hpcadmin),254(hpc),702(techgrp),23171(hpcapps),23173(hpctrain),42124(hpc-vasp),44679(hpc-reems),47919(hpc-sys),61860(rsmadmins)
>  
>
> > > 
> > > The directories and software that I have mentioned are owned by the 
> hpcapps group.  Do I need to have that be my "effective" group for the sage 
> python to work? 
> > > 
> > > Cindy 
> > > 
> > > -- 
> > > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> > > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-devel+...@googlegroups.com. 
> > > To post to this group, send email to sage-...@googlegroups.com. 
> > > Visit this group at http://groups.google.com/group/sage-devel. 
> > > For more options, visit https://groups.google.com/d/optout. 
> > 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
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> an email to sage-devel+...@googlegroup

Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[Francois Bissey]

Nothing to do apart from “make”.
> On 9/01/2015, at 10:21, crooksc...@gmail.com wrote:
> 
> Thank you.  I will give it a try.  
> 
> Pardon my ignorance, but is there anything I have to do to pick up the "make" 
> where I left off?  Or, do I need to start from the beginning?
> 
> Cindy
> 
> On Thursday, January 8, 2015 at 2:41:12 PM UTC-6, François wrote:
> Not completely sure since the error is about the folder’s group permission 
> but that’s worth a try. 
> I am not sure how the “security” stuff has been implemented, it may be that 
> the group is outside 
> a deemed safe range. 
> Hum, this was implemented here: 
> https://github.com/sagemath/sage/blob/master/build/pkgs/python/patches/sys_path_security.patch#L251
>  
> I am guessing in your case the group is writable which of course you want 
> (Fellow HPC admin here). 
> A strategy would be to build in personal directory and then install. 
> 
> François 
> 
> > On 9/01/2015, at 09:26, crook...@gmail.com wrote: 
> > 
> > 
> > 
> > O 
> > I am part of the root  group.  Below is the list of groups that I am part 
> > of: 
> > 
> >   gid=255(hpcadmin) 
> > groups=255(hpcadmin),254(hpc),702(techgrp),23171(hpcapps),23173(hpctrain),42124(hpc-vasp),44679(hpc-reems),47919(hpc-sys),61860(rsmadmins)
> >  
> > 
> > The directories and software that I have mentioned are owned by the hpcapps 
> > group.  Do I need to have that be my "effective" group for the sage python 
> > to work? 
> > 
> > Cindy 
> > 
> > -- 
> > You received this message because you are subscribed to the Google Groups 
> > "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send an 
> > email to sage-devel+...@googlegroups.com. 
> > To post to this group, send email to sage-...@googlegroups.com. 
> > Visit this group at http://groups.google.com/group/sage-devel. 
> > For more options, visit https://groups.google.com/d/optout. 
> 
> 
> -- 
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Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[crookscj02]

Thank you.  I will give it a try.  

Pardon my ignorance, but is there anything I have to do to pick up the 
"make" where I left off?  Or, do I need to start from the beginning?

Cindy

On Thursday, January 8, 2015 at 2:41:12 PM UTC-6, François wrote:
>
> Not completely sure since the error is about the folder’s group permission 
> but that’s worth a try. 
> I am not sure how the “security” stuff has been implemented, it may be 
> that the group is outside 
> a deemed safe range. 
> Hum, this was implemented here: 
>
> https://github.com/sagemath/sage/blob/master/build/pkgs/python/patches/sys_path_security.patch#L251
>  
> I am guessing in your case the group is writable which of course you want 
> (Fellow HPC admin here). 
> A strategy would be to build in personal directory and then install. 
>
> François 
>
> > On 9/01/2015, at 09:26, crook...@gmail.com  wrote: 
> > 
> > 
> > 
> > O 
> > I am part of the root  group.  Below is the list of groups that I am 
> part of: 
> > 
> >   gid=255(hpcadmin) 
> groups=255(hpcadmin),254(hpc),702(techgrp),23171(hpcapps),23173(hpctrain),42124(hpc-vasp),44679(hpc-reems),47919(hpc-sys),61860(rsmadmins)
>  
>
> > 
> > The directories and software that I have mentioned are owned by the 
> hpcapps group.  Do I need to have that be my "effective" group for the sage 
> python to work? 
> > 
> > Cindy 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an email to sage-devel+...@googlegroups.com . 
> > To post to this group, send email to sage-...@googlegroups.com 
> . 
> > Visit this group at http://groups.google.com/group/sage-devel. 
> > For more options, visit https://groups.google.com/d/optout. 
>
>

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Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[Francois Bissey]

Not completely sure since the error is about the folder’s group permission but 
that’s worth a try.
I am not sure how the “security” stuff has been implemented, it may be that the 
group is outside
a deemed safe range.
Hum, this was implemented here:
https://github.com/sagemath/sage/blob/master/build/pkgs/python/patches/sys_path_security.patch#L251
I am guessing in your case the group is writable which of course you want 
(Fellow HPC admin here).
A strategy would be to build in personal directory and then install.

François

> On 9/01/2015, at 09:26, crooksc...@gmail.com wrote:
> 
> 
> 
> O
> I am part of the root  group.  Below is the list of groups that I am part of:
> 
>   gid=255(hpcadmin) 
> groups=255(hpcadmin),254(hpc),702(techgrp),23171(hpcapps),23173(hpctrain),42124(hpc-vasp),44679(hpc-reems),47919(hpc-sys),61860(rsmadmins)
> 
> The directories and software that I have mentioned are owned by the hpcapps 
> group.  Do I need to have that be my "effective" group for the sage python to 
> work?
> 
> Cindy
> 
> -- 
> You received this message because you are subscribed to the Google Groups 
> "sage-devel" group.
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Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[crookscj02]

OSorry, I should have said I am NOT part of the root group.  I was typing 
too fast.

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Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[crookscj02]

O

> I am part of the root  group.  Below is the list of groups that I am part 
> of:
>

  gid=255(hpcadmin) 
groups=255(hpcadmin),254(hpc),702(techgrp),23171(hpcapps),23173(hpctrain),42124(hpc-vasp),44679(hpc-reems),47919(hpc-sys),61860(rsmadmins)

The directories and software that I have mentioned are owned by the hpcapps 
group.  Do I need to have that be my "effective" group for the sage python 
to work?

Cindy

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Re: [sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[Francois Bissey]

That’s interesting, would you belong to an admin group or even the root group?
Or more likely you set the group ownership and permission for this folder to 
something that’s
not acceptable for the python shipped by sage.

François
> On 9/01/2015, at 08:43, crooksc...@gmail.com wrote:
> 
> I am trying to compile sage-6.4.1 for one of my users.  I am working on a 
> SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my personal 
> account and I own the build directory and all of the directories/files for 
> gcc and python.  I am still getting the following error:
> 
> checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not 
> adding
>  directory '' to sys.path since it's writable by an untrusted group.
> Untrusted users could put files in this directory which might then be 
> imported b
> y your Python code. As a general precaution from similar exploits, you should 
> no
> t execute Python code from this directory
> 
> I have attached the sage_pynac-0.3.2.log for you to review.  I have tried 
> looking through previous posts, but I don't see anything that quite matches 
> this situation.
> 
> Thanks in advance for your help.
> 
> Cindy
> 
> -- 
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[sage-devel] Build error for sage-6.4.1 in pynac-0.3.2

[crookscj02]

I am trying to compile sage-6.4.1 for one of my users.  I am working on a 
SLES11 SP2 machine using gcc 4.9.2 and python 2.7.7.  I am using my 
personal account and I own the build directory and all of the 
directories/files for gcc and python.  I am still getting the following 
error:

checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not 
adding
 directory '' to sys.path since it's writable by an untrusted group.
Untrusted users could put files in this directory which might then be 
imported b
y your Python code. As a general precaution from similar exploits, you 
should no
t execute Python code from this directory

I have attached the sage_pynac-0.3.2.log for you to review.  I have tried 
looking through previous posts, but I don't see anything that quite matches 
this situation.

Thanks in advance for your help.

Cindy

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pynac-0.3.2

Setting up build directory for pynac-0.3.2
Finished set up

Host system:
Linux hpcbuild02 3.0.13-0.27-default #1 SMP Wed Feb 15 13:33:49 UTC 2012 (d73692b) x86_64 x86_64 x86_64 GNU/Linux

C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/hpc/apps/SLES/3.0/x86_64/gcc/4.9.2/libexec/gcc/x86_64-linux-gnu/4.9.2/lto-wrapper
Target: x86_64-linux-gnu
Configured with: ../gcc-4.9.2//configure --build=x86_64-linux-gnu --prefix=/hpc/apps/SLES/3.0/x86_64/gcc/4.9.2 --with-gmp=/hpc/apps/SLES/3.0/x86_64/gmp/5.1.3 --with-mpfr=/hpc/apps/SLES/3.0/x86_64/mpfr/3.1.2 --with-mpc=/hpc/apps/SLES/3.0/x86_64/mpc/1.0.1 --enable-checking-release --enable-languages=c,c++,fortran --disable-multilib --program-suffix=4.9.2
Thread model: posix
gcc version 4.9.2 (GCC) 

Starting build...
Running build_pynac...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for style of include used by make... GNU
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for python... /hpc/tstapps/src/sage/sage-6.4.1/local/bin/python
checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not adding directory '' to sys.path since it's writable by an untrusted group.
Untrusted users could put files in this directory which might then be imported by your Python code. As a general precaution from similar exploits, you should not execute Python code from this directory
yes
checking for the distutils Python package... no
configure: error: cannot import Python module "distutils".
Please check your Python installation. The error was:
sys:1: RuntimeWarning: not adding directory '' to sys.path since it's writable by an untrusted group.
Untrusted users could put files in this directory which might then be imported by your Python code. As a general precaution from similar exploits, you should not execute Python code from this directory
make[3]: Entering directory `/hpc/tstapps/src/sage/sage-6.4.1/local/var/tmp/sage/build/pynac-0.3.2/src'
make[3]: *** No targets specified and no makefile found.  Stop.
make[3]: Leaving directory `/hpc/tstapps/src/sage/sage-6.4.1/local/var/tmp/sage/build/pynac-0.3.2/src'
Error building pynac.

real0m0.926s
user0m0.240s
sys 0m0.180s

Error installing package pynac-0.3.2

Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
  /hpc/tstapps/src/sage/sage-6.4.1/logs/pkgs/pynac-0.3.2.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/hpc/tstapps/src/sage/sage-6.4.1/local/var/tmp/sage/build/pynac-0.3.2 and type 'make' or whatever is appropriate.
Instead, the following commands setup all env

Re: [sage-devel] Build error in Sage-6.2: pynac-0.3.2

[kksurendran]

configure: error: cannot import Python module "distutils".

It is not  a permission problem as shown by the above line in the log.
I have explained the matter in a new post as the same situation prevails in 
sage-6.4.

On Saturday, 7 June 2014 02:22:13 UTC-4, vdelecroix wrote:
>
> From your logs it seems to be a permission problem. What user own 
> /opt/sage-6.2 ? and what are the permissions ? 
>
> 2014-06-07 3:15 UTC+02:00, Alasdair >: 
> > Here's the error as reported during the compilation process: 
> > 
> > checking for python... /opt/sage-6.2/local/bin/python 
> >> checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: 
> not 
> >> 
> >> adding directory '' to sys.path since it's writable by an untrusted 
> >> group. 
> >> Untrusted users could put files in this directory which might then be 
> >> imported by your Python code. As a general precaution from similar 
> >> exploits, you should not execute Python code from this directory 
> >> yes 
> >> checking for the distutils Python package... no 
> >> configure: error: cannot import Python module "distutils". 
> >> Please check your Python installation. The error was: 
> >> sys:1: RuntimeWarning: not adding directory '' to sys.path since it's 
> >> writable by an untrusted group. 
> >> Untrusted users could put files in this directory which might then be 
> >> imported by your Python code. As a general precaution from similar 
> >> exploits, you should not execute Python code from this directory 
> >> make[3]: Entering directory 
> >> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src' 
> >> make[3]: *** No targets specified and no makefile found.  Stop. 
> >> make[3]: Leaving directory 
> >> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src' 
> >> Error building pynac. 
> >> 
> >> real0m0.869s 
> >> user0m0.528s 
> >> sys 0m0.384s 
> >> 
>  
> >> Error installing package pynac-0.3.2 
> >> 
>  
> >> Please email sage-devel (http://groups.google.com/group/sage-devel) 
> >> explaining the problem and including the relevant part of the log file 
> >>   /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log 
> >> Describe your computer, operating system, etc. 
> >> If you want to try to fix the problem yourself, *don't* just cd to 
> >> /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 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 '/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2' && 
> >> '/opt/sage-6.2/sage' --sh) 
> >> When you are done debugging, you can type "exit" to leave the subshell. 
> >> 
>  
> >> make[2]: *** [/opt/sage-6.2/local/var/lib/sage/installed/pynac-0.3.2] 
> >> Error 1 
> >> make[2]: Leaving directory `/opt/sage-6.2/build' 
> >> make[1]: *** [all] Error 2 
> >> make[1]: Leaving directory `/opt/sage-6.2/build' 
> >> 
> >> real150m50.768s 
> >> user131m18.168s 
> >> sys 17m8.948s 
> >> *** 
> >> Error building Sage. 
> >> 
> >> The following package(s) may have failed to build: 
> >> 
> >> package: pynac-0.3.2 
> >> log file: /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log 
> >> build directory: /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 
> >> 
> >> 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: *** [build] Error 1 
> >> 
> > 
> > I'm attempting this on a new installation of kubuntu 14.04 64-bit.  This 
> is 
> > 
> > the first time, in maybe 20 Sage compilations over the years, that I've 
> > encountered an error.  I've aso checked that I do have distutils, it was 
> > installed when I installed Python initially (version 2.7); there is also 
> > distutils for Python 3.4; I imagine loaded as part of the Sage compile 
> > process. 
> > 
> > Any advice? 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to sage-devel+...@googlegroups.com . 
> > To post to this group, send email to sage-...@googlegroups.com 
> . 
> > Visit this group at http://groups.google.com/group/sage-devel. 
> > For more options, visit https://groups.google.com/d/optout. 
> > 
>

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To po

Re: [sage-devel] Build error in Sage-6.2: pynac-0.3.2

[Montgomery-Smith, Stephen]

Hey people,

FreeBSD people do like to build their ports as root.  The problem
described below could be easily fixed by simply removing the group write
permissions of all the files in the tarball upstream/pynac-0.3.2.tar.bz2.

It's not such a great deal if this isn't fixed by the time sage-6.3
comes out, but it would be nice.

On 06/06/2014 08:15 PM, Alasdair wrote:
> Here's the error as reported during the compilation process:
> 
> checking for python... /opt/sage-6.2/local/bin/python
> checking for a version of Python >= '2.1.0'... sys:1:
> RuntimeWarning: not adding directory '' to sys.path since it's
> writable by an untrusted group.
> Untrusted users could put files in this directory which might then
> be imported by your Python code. As a general precaution from
> similar exploits, you should not execute Python code from this directory
> yes
> checking for the distutils Python package... no
> configure: error: cannot import Python module "distutils".
> Please check your Python installation. The error was:
> sys:1: RuntimeWarning: not adding directory '' to sys.path since
> it's writable by an untrusted group.
> Untrusted users could put files in this directory which might then
> be imported by your Python code. As a general precaution from
> similar exploits, you should not execute Python code from this directory
> make[3]: Entering directory
> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
> make[3]: *** No targets specified and no makefile found.  Stop.
> make[3]: Leaving directory
> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
> Error building pynac.
> 
> real0m0.869s
> user0m0.528s
> sys 0m0.384s
> 
> Error installing package pynac-0.3.2
> 
> Please email sage-devel (http://groups.google.com/group/sage-devel)
> explaining the problem and including the relevant part of the log file
>   /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
> Describe your computer, operating system, etc.
> If you want to try to fix the problem yourself, *don't* just cd to
> /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 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 '/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2' &&
> '/opt/sage-6.2/sage' --sh)
> When you are done debugging, you can type "exit" to leave the subshell.
> 
> make[2]: ***
> [/opt/sage-6.2/local/var/lib/sage/installed/pynac-0.3.2] Error 1
> make[2]: Leaving directory `/opt/sage-6.2/build'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/opt/sage-6.2/build'
> 
> real150m50.768s
> user131m18.168s
> sys 17m8.948s
> ***
> Error building Sage.
> 
> The following package(s) may have failed to build:
> 
> package: pynac-0.3.2
> log file: /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
> build directory: /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2
> 
> 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: *** [build] Error 1
> 
> 
> I'm attempting this on a new installation of kubuntu 14.04 64-bit.  This
> is the first time, in maybe 20 Sage compilations over the years, that
> I've encountered an error.  I've aso checked that I do have distutils,
> it was installed when I installed Python initially (version 2.7); there
> is also distutils for Python 3.4; I imagine loaded as part of the Sage
> compile process.
> 
> Any advice?
> 
> -- 
> You received this message because you are subscribed to the Google
> Groups "sage-devel" group.
> To unsubscribe from this group and stop receiving emails from it, send
> an email to sage-devel+unsubscr...@googlegroups.com
> .
> To post to this group, send email to sage-devel@googlegroups.com
> .
> Visit this group at http://groups.google.com/group/sage-devel.
> For more options, visit https://groups.google.com/d/optout.

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Re: [sage-devel] Build error in Sage-6.2: pynac-0.3.2

[Vincent Delecroix]

Have a look at the commands
 chown: change the owner/group
 chmod: change permissions

What you have to do is to make /opt/sage-6.2 writable by you, not the
whole /opt. The simplest way, assuming that your username is alasdair,
is to change the owner of everything in /opt/sage-6.2 with

sudo chown -R alasdair:alasdair /opt/sage-6.2

and then run make as alasdair.


2014-06-07 9:35 UTC+02:00, Alasdair :
> Thanks for that - I compiled it as root, so that it could write to the
> directory /opt/sage-6.2.  There should have been no permission problems.
> (In essence, I did what I've always done: opened up a login shell as root,
> and installed sage in the directory /opt/sage-x.y.
>
> However!  I've just discovered a series of posts on this very topic:
> https://groups.google.com/forum/#!topic/sage-support/H-SI3700rGc and it
> seems that the trick is to compile Sage as non-root.  I wonder what the
> best way to do that is; I don't want Sage and all of its bits cluttering up
>
> my home directory, which I like to keep streamlined.  Maybe if I make the
> /opt directory writable by me... I'll keep you posted!
>
> Thanks,
> Alasdair
>
> On Saturday, 7 June 2014 16:22:13 UTC+10, vdelecroix wrote:
>>
>> From your logs it seems to be a permission problem. What user own
>> /opt/sage-6.2 ? and what are the permissions ?
>>
>> 2014-06-07 3:15 UTC+02:00, Alasdair >:
>> > Here's the error as reported during the compilation process:
>> >
>> > checking for python... /opt/sage-6.2/local/bin/python
>> >> checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning:
>> not
>> >>
>> >> adding directory '' to sys.path since it's writable by an untrusted
>> >> group.
>> >> Untrusted users could put files in this directory which might then be
>> >> imported by your Python code. As a general precaution from similar
>> >> exploits, you should not execute Python code from this directory
>> >> yes
>> >> checking for the distutils Python package... no
>> >> configure: error: cannot import Python module "distutils".
>> >> Please check your Python installation. The error was:
>> >> sys:1: RuntimeWarning: not adding directory '' to sys.path since it's
>> >> writable by an untrusted group.
>> >> Untrusted users could put files in this directory which might then be
>> >> imported by your Python code. As a general precaution from similar
>> >> exploits, you should not execute Python code from this directory
>> >> make[3]: Entering directory
>> >> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
>> >> make[3]: *** No targets specified and no makefile found.  Stop.
>> >> make[3]: Leaving directory
>> >> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
>> >> Error building pynac.
>> >>
>> >> real0m0.869s
>> >> user0m0.528s
>> >> sys 0m0.384s
>> >>
>> 
>> >> Error installing package pynac-0.3.2
>> >>
>> 
>> >> Please email sage-devel (http://groups.google.com/group/sage-devel)
>> >> explaining the problem and including the relevant part of the log file
>> >>
>> >>   /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
>> >> Describe your computer, operating system, etc.
>> >> If you want to try to fix the problem yourself, *don't* just cd to
>> >> /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 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 '/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2' &&
>> >> '/opt/sage-6.2/sage' --sh)
>> >> When you are done debugging, you can type "exit" to leave the subshell.
>> >>
>> >>
>> 
>> >> make[2]: *** [/opt/sage-6.2/local/var/lib/sage/installed/pynac-0.3.2]
>> >> Error 1
>> >> make[2]: Leaving directory `/opt/sage-6.2/build'
>> >> make[1]: *** [all] Error 2
>> >> make[1]: Leaving directory `/opt/sage-6.2/build'
>> >>
>> >> real150m50.768s
>> >> user131m18.168s
>> >> sys 17m8.948s
>> >> ***
>> >> Error building Sage.
>> >>
>> >> The following package(s) may have failed to build:
>> >>
>> >> package: pynac-0.3.2
>> >> log file: /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
>> >> build directory: /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2
>> >>
>> >> 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: *** [build] Error 1
>> >>
>> >
>> > I'm attempting this on a new installation of kubuntu 14.04 64-bit.  This
>> >
>> is
>> >
>> > the first time, in maybe 20 Sage compilations over the years, that I've
>> >
>> > encou

Re: [sage-devel] Build error in Sage-6.2: pynac-0.3.2

[Alasdair]

Thanks for that - I compiled it as root, so that it could write to the 
directory /opt/sage-6.2.  There should have been no permission problems.  
(In essence, I did what I've always done: opened up a login shell as root, 
and installed sage in the directory /opt/sage-x.y.  

However!  I've just discovered a series of posts on this very topic: 
https://groups.google.com/forum/#!topic/sage-support/H-SI3700rGc and it 
seems that the trick is to compile Sage as non-root.  I wonder what the 
best way to do that is; I don't want Sage and all of its bits cluttering up 
my home directory, which I like to keep streamlined.  Maybe if I make the 
/opt directory writable by me... I'll keep you posted!

Thanks,
Alasdair

On Saturday, 7 June 2014 16:22:13 UTC+10, vdelecroix wrote:
>
> From your logs it seems to be a permission problem. What user own 
> /opt/sage-6.2 ? and what are the permissions ? 
>
> 2014-06-07 3:15 UTC+02:00, Alasdair >: 
> > Here's the error as reported during the compilation process: 
> > 
> > checking for python... /opt/sage-6.2/local/bin/python 
> >> checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: 
> not 
> >> 
> >> adding directory '' to sys.path since it's writable by an untrusted 
> >> group. 
> >> Untrusted users could put files in this directory which might then be 
> >> imported by your Python code. As a general precaution from similar 
> >> exploits, you should not execute Python code from this directory 
> >> yes 
> >> checking for the distutils Python package... no 
> >> configure: error: cannot import Python module "distutils". 
> >> Please check your Python installation. The error was: 
> >> sys:1: RuntimeWarning: not adding directory '' to sys.path since it's 
> >> writable by an untrusted group. 
> >> Untrusted users could put files in this directory which might then be 
> >> imported by your Python code. As a general precaution from similar 
> >> exploits, you should not execute Python code from this directory 
> >> make[3]: Entering directory 
> >> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src' 
> >> make[3]: *** No targets specified and no makefile found.  Stop. 
> >> make[3]: Leaving directory 
> >> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src' 
> >> Error building pynac. 
> >> 
> >> real0m0.869s 
> >> user0m0.528s 
> >> sys 0m0.384s 
> >> 
>  
> >> Error installing package pynac-0.3.2 
> >> 
>  
> >> Please email sage-devel (http://groups.google.com/group/sage-devel) 
> >> explaining the problem and including the relevant part of the log file 
> >>   /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log 
> >> Describe your computer, operating system, etc. 
> >> If you want to try to fix the problem yourself, *don't* just cd to 
> >> /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 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 '/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2' && 
> >> '/opt/sage-6.2/sage' --sh) 
> >> When you are done debugging, you can type "exit" to leave the subshell. 
> >> 
>  
> >> make[2]: *** [/opt/sage-6.2/local/var/lib/sage/installed/pynac-0.3.2] 
> >> Error 1 
> >> make[2]: Leaving directory `/opt/sage-6.2/build' 
> >> make[1]: *** [all] Error 2 
> >> make[1]: Leaving directory `/opt/sage-6.2/build' 
> >> 
> >> real150m50.768s 
> >> user131m18.168s 
> >> sys 17m8.948s 
> >> *** 
> >> Error building Sage. 
> >> 
> >> The following package(s) may have failed to build: 
> >> 
> >> package: pynac-0.3.2 
> >> log file: /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log 
> >> build directory: /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 
> >> 
> >> 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: *** [build] Error 1 
> >> 
> > 
> > I'm attempting this on a new installation of kubuntu 14.04 64-bit.  This 
> is 
> > 
> > the first time, in maybe 20 Sage compilations over the years, that I've 
> > encountered an error.  I've aso checked that I do have distutils, it was 
> > installed when I installed Python initially (version 2.7); there is also 
> > distutils for Python 3.4; I imagine loaded as part of the Sage compile 
> > process. 
> > 
> > Any advice? 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "sage-devel" group. 
> > To unsubscribe from this group and stop receiving emails from it, se

Re: [sage-devel] Build error in Sage-6.2: pynac-0.3.2

[Vincent Delecroix]

>From your logs it seems to be a permission problem. What user own
/opt/sage-6.2 ? and what are the permissions ?

2014-06-07 3:15 UTC+02:00, Alasdair :
> Here's the error as reported during the compilation process:
>
> checking for python... /opt/sage-6.2/local/bin/python
>> checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not
>>
>> adding directory '' to sys.path since it's writable by an untrusted
>> group.
>> Untrusted users could put files in this directory which might then be
>> imported by your Python code. As a general precaution from similar
>> exploits, you should not execute Python code from this directory
>> yes
>> checking for the distutils Python package... no
>> configure: error: cannot import Python module "distutils".
>> Please check your Python installation. The error was:
>> sys:1: RuntimeWarning: not adding directory '' to sys.path since it's
>> writable by an untrusted group.
>> Untrusted users could put files in this directory which might then be
>> imported by your Python code. As a general precaution from similar
>> exploits, you should not execute Python code from this directory
>> make[3]: Entering directory
>> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
>> make[3]: *** No targets specified and no makefile found.  Stop.
>> make[3]: Leaving directory
>> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
>> Error building pynac.
>>
>> real0m0.869s
>> user0m0.528s
>> sys 0m0.384s
>> 
>> Error installing package pynac-0.3.2
>> 
>> Please email sage-devel (http://groups.google.com/group/sage-devel)
>> explaining the problem and including the relevant part of the log file
>>   /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
>> Describe your computer, operating system, etc.
>> If you want to try to fix the problem yourself, *don't* just cd to
>> /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 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 '/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2' &&
>> '/opt/sage-6.2/sage' --sh)
>> When you are done debugging, you can type "exit" to leave the subshell.
>> 
>> make[2]: *** [/opt/sage-6.2/local/var/lib/sage/installed/pynac-0.3.2]
>> Error 1
>> make[2]: Leaving directory `/opt/sage-6.2/build'
>> make[1]: *** [all] Error 2
>> make[1]: Leaving directory `/opt/sage-6.2/build'
>>
>> real150m50.768s
>> user131m18.168s
>> sys 17m8.948s
>> ***
>> Error building Sage.
>>
>> The following package(s) may have failed to build:
>>
>> package: pynac-0.3.2
>> log file: /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
>> build directory: /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2
>>
>> 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: *** [build] Error 1
>>
>
> I'm attempting this on a new installation of kubuntu 14.04 64-bit.  This is
>
> the first time, in maybe 20 Sage compilations over the years, that I've
> encountered an error.  I've aso checked that I do have distutils, it was
> installed when I installed Python initially (version 2.7); there is also
> distutils for Python 3.4; I imagine loaded as part of the Sage compile
> process.
>
> Any advice?
>
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[sage-devel] Build error in Sage-6.2: pynac-0.3.2

[Alasdair]

Here's the error as reported during the compilation process:

checking for python... /opt/sage-6.2/local/bin/python
> checking for a version of Python >= '2.1.0'... sys:1: RuntimeWarning: not 
> adding directory '' to sys.path since it's writable by an untrusted group.
> Untrusted users could put files in this directory which might then be 
> imported by your Python code. As a general precaution from similar 
> exploits, you should not execute Python code from this directory
> yes
> checking for the distutils Python package... no
> configure: error: cannot import Python module "distutils".
> Please check your Python installation. The error was:
> sys:1: RuntimeWarning: not adding directory '' to sys.path since it's 
> writable by an untrusted group.
> Untrusted users could put files in this directory which might then be 
> imported by your Python code. As a general precaution from similar 
> exploits, you should not execute Python code from this directory
> make[3]: Entering directory 
> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
> make[3]: *** No targets specified and no makefile found.  Stop.
> make[3]: Leaving directory 
> `/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2/src'
> Error building pynac.
>
> real0m0.869s
> user0m0.528s
> sys 0m0.384s
> 
> Error installing package pynac-0.3.2
> 
> Please email sage-devel (http://groups.google.com/group/sage-devel)
> explaining the problem and including the relevant part of the log file
>   /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
> Describe your computer, operating system, etc.
> If you want to try to fix the problem yourself, *don't* just cd to
> /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2 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 '/opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2' && 
> '/opt/sage-6.2/sage' --sh)
> When you are done debugging, you can type "exit" to leave the subshell.
> 
> make[2]: *** [/opt/sage-6.2/local/var/lib/sage/installed/pynac-0.3.2] 
> Error 1
> make[2]: Leaving directory `/opt/sage-6.2/build'
> make[1]: *** [all] Error 2
> make[1]: Leaving directory `/opt/sage-6.2/build'
>
> real150m50.768s
> user131m18.168s
> sys 17m8.948s
> ***
> Error building Sage.
>
> The following package(s) may have failed to build:
>
> package: pynac-0.3.2
> log file: /opt/sage-6.2/logs/pkgs/pynac-0.3.2.log
> build directory: /opt/sage-6.2/local/var/tmp/sage/build/pynac-0.3.2
>
> 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: *** [build] Error 1
>

I'm attempting this on a new installation of kubuntu 14.04 64-bit.  This is 
the first time, in maybe 20 Sage compilations over the years, that I've 
encountered an error.  I've aso checked that I do have distutils, it was 
installed when I installed Python initially (version 2.7); there is also 
distutils for Python 3.4; I imagine loaded as part of the Sage compile 
process.

Any advice?

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Re: [sage-devel] Build error on 5.12

[Owen Campbell]

Aha - thank you!! I hadn't spotted that.

On Friday, December 6, 2013 12:51:36 PM UTC, Jeroen Demeyer wrote:
>
> On 2013-12-06 12:50, Owen Campbell wrote: 
> > This is on a Macbook running Mavericks. 
> Mavericks is not yet supported, but it should be supported in the 
> upcoming Sage 5.13 version. If you're feeling adventurous, you can check 
> out http://trac.sagemath.org/sage_trac/ticket/15433 
>

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Re: [sage-devel] Build error on 5.12

[Jeroen Demeyer]

On 2013-12-06 12:50, Owen Campbell wrote:

This is on a Macbook running Mavericks.
Mavericks is not yet supported, but it should be supported in the 
upcoming Sage 5.13 version. If you're feeling adventurous, you can check 
out http://trac.sagemath.org/sage_trac/ticket/15433


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[sage-devel] Build error on 5.12

[Owen Campbell]

Hi,

I'm completely new to sage and attempting to build it from source for the first 
time.

I've hit the following build error:

checking for uintptr_t... yes
checking for the GMP library version 4.1.3 or above... no
configure: error: Cannot find GMP version 4.1.3 or higher.
GMP is the GNU Multi-Precision library:
see http://www.swox.com/gmp/ for more information.
When compiling the GMP library, do not forget to enable the C++ interface:
add --enable-cxx to the configuration options.
Error configuring the Parma Polyhedra Library.

real0m35.367s
user0m9.663s
sys 0m7.359s

Error installing package ppl-1.1pre9.p0


This is on a Macbook running Mavericks.

Have a missed a pre-requisite somewhere?

Many thanks for any help,

Owen

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Re: [sage-devel] build error of flint on opensuse 12.2 (x86_64)

[Shahab Asgharzadeh]

Hi Jeroen,

Sorry for the delay, here is the output you requested 
>From shell:
linux-vdso.so.1 (0x7fffd39e8000)
libmpc.so.3 => not found
libmpfr.so.4 => /usr/lib64/libmpfr.so.4 (0x7fa61e11)
libgmp.so.11 => not found
libdl.so.2 => /lib64/libdl.so.2 (0x7fa61df08000)
libz.so.1 => /lib64/libz.so.1 (0x7fa61dcf)
libm.so.6 => /lib64/libm.so.6 (0x7fa61d9f8000)
libc.so.6 => /lib64/libc.so.6 (0x7fa61d65)
libgmp.so.10 => /usr/lib64/libgmp.so.10 (0x7fa61d3d)
/lib64/ld-linux-x86-64.so.2 (0x7fa61e37)

from sage -sh
linux-vdso.so.1 (0x7fff9f80)
libmpc.so.3 => /data2/sage-5.11/local/lib64/libmpc.so.3 
(0x7ffa6c5b)
libmpfr.so.4 => /data2/sage-5.11/local/lib/libmpfr.so.4 
(0x7ffa6c35)
libgmp.so.11 => /data2/sage-5.11/local/lib/libgmp.so.11 
(0x7ffa6c0e)
libdl.so.2 => /lib64/libdl.so.2 (0x7ffa6beb8000)
libz.so.1 => /data2/sage-5.11/local/lib/libz.so.1 (0x7ffa6bca)
libm.so.6 => /lib64/libm.so.6 (0x7ffa6b9a8000)
libc.so.6 => /lib64/libc.so.6 (0x7ffa6b60)
/lib64/ld-linux-x86-64.so.2 (0x7ffa6c7c8000)

I believe I did use j > 1 during the build but I can't remember.  I will 
try to recompile with just make for both 5.11 and 5.10 to see if it works.

Thanks!


On Thursday, September 26, 2013 9:02:16 AM UTC-7, Jeroen Demeyer wrote:
>
> 1) Please give the output of the following command, both from a normal 
> shell and from within the Sage shell (sage --sh): 
>
> $ ldd /data2/sage-5.11/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.3/cc1 
>
> 2) Is the error reproducible (does it happen again if you run "make")? 
>
> 3) Did you use MAKE="make -jN" with N > 1? If yes, please send me the 
> whole install.log, as the error might be a race condition with parallel 
> builds. 
>

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Re: [sage-devel] build error of flint on opensuse 12.2 (x86_64)

[Jeroen Demeyer]

1) Please give the output of the following command, both from a normal 
shell and from within the Sage shell (sage --sh):


$ ldd /data2/sage-5.11/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.3/cc1

2) Is the error reproducible (does it happen again if you run "make")?

3) Did you use MAKE="make -jN" with N > 1? If yes, please send me the 
whole install.log, as the error might be a race condition with parallel 
builds.


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[sage-devel] build error of flint on opensuse 12.2 (x86_64)

[Shahab Asgharzadeh]

I tried building in from source and this is the error I got.  any help would be 
greatly appreciated.

Thanks!

Shahab




C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/data2/sage-5.11/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.3/lto-wrapper
Target: x86_64-unknown-linux-gnu
Configured with: ../src/configure --prefix=/data2/sage-5.11/local 
--with-local-prefix=/data2/sage-5.11/local --w
ith-gmp=/data2/sage-5.11/local --with-mpfr=/data2/sage-5.11/local 
--with-mpc=/data2/sage-5.11/local --with-syste
m-zlib --disable-multilib --disable-nls  
Thread model: posix
gcc version 4.7.3 (GCC) 

Patching FLINT.
patching file configure
patching file configure
Configuring FLINT.
Configuring...x86_64-Linux
Testing __builtin_popcountl...yes
Testing native popcount...yes
Building FLINT shared library.
make[3]: Entering directory `/data2/sage-5.11/spkg/build/flint-2.3.p1/src'
if [ "1" -eq "1" ]; then \
make libflint.so; \
fi
make[4]: Entering directory `/data2/sage-5.11/spkg/build/flint-2.3.p1/src'
gcc -fPIC -O2 -g -ansi -pedantic -Wall -mpopcnt  -funroll-loops 
-I/data2/sage-5.11/spkg/build/flint-2.3.p1/src -
I/data2/sage-5.11/local/include -I/data2/sage-5.11/local/include 
-I/data2/sage-5.11/local/include -c clz_tab.c -
o build/clz_tab.lo;
/data2/sage-5.11/local/lib/gcc/x86_64-unknown-linux-gnu/4.7.3/cc1: error while 
loading shared libraries: libmpc.
so.3: cannot open shared object file: No such file or directory
make[4]: *** [build/clz_tab.lo] Error 1
make[4]: Leaving directory `/data2/sage-5.11/spkg/build/flint-2.3.p1/src'
make[3]: *** [library] Error 2
make[3]: Leaving directory `/data2/sage-5.11/spkg/build/flint-2.3.p1/src'
Error: Failed to build FLINT shared library.

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[sage-devel] Build Error in gf2x package on AMD Athlon XP 2600+

[Andrew Fiori]

This is likely a build error bug on all systems which do not support SSE2 but 
where building is done using the current version of gcc. It may also manifest 
as a runtime error on binary builds installed on systems which do not support 
SSE2 (but I have not tested that).

I am submitting this here rather than to bug tracker for several reasons:
   - It is unlikely anyone cares enough to fix this properly upstream (which is 
where the bug really is).
   - The build error only effects building from source on systems that are out 
of date and will becoming even less common going forward.

I am mentioning it at all, because it will help anyone who comes across this 
error in the future. The same type of error may cause somewhat confusing 
runtime errors in other packages (bug tracker searches suggest this type of 
issue has come up before in other packages).

The bug:
  The bug is somewhere in the gf2x build scripts "src/config/acinclude.m4" or 
"src/configure" somehow it decides whether or not the system supports sse2 
(look around line 75 of acinclude.m4. It appears to do this by checking if gcc 
can compile something that uses sse2. It turns out that it can... even if the 
system you are on cannot. Consequently it tries to build everything with sse2. 
This causes a problem when it tries to tune itself "src/src/tune-lowlevel.pl". 
Around line 70-78 it tries to run the compiled code. Most of these don't 
require sse2 really, and so work, some do (mul3t, mul3k, mul3k2) these fail, it 
then can't pick which one to use, and terminates building.
   If there are other places in sage where similar sse2 detection is used, but 
which are not executed at build time (most things are not), then sage will 
encounter unexpected runtime bugs when pieces of code that can benefit from 
sse2 are used.
   

The solution:
   gf2x doesn't require sse2 to work. The easiest way to build it on a system 
where the above bug is encountered is to modify:
   spkg-install:38 to become:
   ./configure --enable-sse2=no --prefix="$SAGE_LOCAL"
You don't really want to do this in the main branch though, as this slows 
things down for the 99+% of people who don't have an archaic system they are 
trying to run sage on.
A better solution is to add an if statement at this place and environment 
variable globally to disable sse2 when it doesn't exist.
Alternatively one could invest the time and figure out then fix gf2x build 
system.

- Andrew

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Re: [sage-devel] Build error for sage 5.5

[Stephen Montgomery-Smith]

On 12/26/2012 11:23 AM, kcrisman wrote:
> 
> 
> On Wednesday, December 26, 2012 6:51:42 AM UTC-5, Jeroen Demeyer wrote:
> 
> On 2012-12-25 20:22, Stephen Montgomery-Smith wrote:
> > When I am building sage-5.5 inside of sage-5.5
> What does this mean? If it means building Sage inside a Sage shell,
> that's not supported and might indeed break.
> 
> 
> I think this means the sage-5.5 spkg in sage-5.5.
> 
> No, the current state of the FreeBSD port is indeed a "port", see
> http://www.freebsd.org/cgi/cvsweb.cgi/ports/math/sage/ 

I was trying to update the port to 5.5.

I think what the problem might be is that when I do the make with
multiple threads, my computer runs out of resources.  Often it quits
inside python with an error "not enough open files."  So I am guessing
that maybe something broke in the making of python or cython, but the
breakage didn't cause the make to stop inside of python or cython, but
rather created a broken python or cython that caused the build error in
sage.

Probably I need to do some tuning to my machine.

Stephen


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Re: [sage-devel] Build error for sage 5.5

[kcrisman]

On Wednesday, December 26, 2012 6:51:42 AM UTC-5, Jeroen Demeyer wrote:
>
> On 2012-12-25 20:22, Stephen Montgomery-Smith wrote: 
> > When I am building sage-5.5 inside of sage-5.5 
> What does this mean? If it means building Sage inside a Sage shell, 
> that's not supported and might indeed break. 
>

I think this means the sage-5.5 spkg in sage-5.5.

No, the current state of the FreeBSD port is indeed a "port", see 
http://www.freebsd.org/cgi/cvsweb.cgi/ports/math/sage/ 

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Re: [sage-devel] Build error for sage 5.5

[Jeroen Demeyer]

On 2012-12-25 20:22, Stephen Montgomery-Smith wrote:
> When I am building sage-5.5 inside of sage-5.5
What does this mean? If it means building Sage inside a Sage shell,
that's not supported and might indeed break.

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Re: [sage-devel] Build error for sage 5.5

[Stephen Montgomery-Smith]

On 12/25/2012 01:22 PM, Stephen Montgomery-Smith wrote:
> When I am building sage-5.5 inside of sage-5.5, I get the following
> error in my build log.  I was able to build sage-5.5.rc1 with no
> problem.  Am I unique with this problem?  I am building under FreeBSD-8.2.
> 
> 
> gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -pipe
> -Wl,-rpath=/usr/ports/math/sage/work/sage-5.5/local/lib
> -Wl,-rpath=/usr/local/lib/gcc46 -fPIC
> -I/usr/ports/math/sage/work/sage-5.5/local/include
> -I/usr/ports/math/sage/work/sage-5.5/local/include/csage
> -I/usr/ports/math/sage/work/sage-5.5/devel/sage/sage/ext
> -I/usr/ports/math/sage/work/sage-5.5/local/include/python2.7 -c
> sage/libs/mpmath/ext_impl.c -o
> build/temp.freebsd-8.3-STABLE-amd64-2.7/sage/libs/mpmath/ext_impl.o -w
> sage/libs/ppl.cpp:286:18: fatal error: ppl.hh: No such file or directory
> 


I probably am unique, because I was unable to reproduce the error.
Sorry for jumping the gun, and sorry for the noise.

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[sage-devel] Build error for sage 5.5

[Stephen Montgomery-Smith]

When I am building sage-5.5 inside of sage-5.5, I get the following
error in my build log.  I was able to build sage-5.5.rc1 with no
problem.  Am I unique with this problem?  I am building under FreeBSD-8.2.


gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -pipe
-Wl,-rpath=/usr/ports/math/sage/work/sage-5.5/local/lib
-Wl,-rpath=/usr/local/lib/gcc46 -fPIC
-I/usr/ports/math/sage/work/sage-5.5/local/include
-I/usr/ports/math/sage/work/sage-5.5/local/include/csage
-I/usr/ports/math/sage/work/sage-5.5/devel/sage/sage/ext
-I/usr/ports/math/sage/work/sage-5.5/local/include/python2.7 -c
sage/libs/mpmath/ext_impl.c -o
build/temp.freebsd-8.3-STABLE-amd64-2.7/sage/libs/mpmath/ext_impl.o -w
sage/libs/ppl.cpp:286:18: fatal error: ppl.hh: No such file or directory

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Re: [sage-devel] build error in schroot+debootstrap

[Jason B Hill]

It actually doesn't appear to give an error then. Under both root and
sageserver users in the chroot, I get the

... stuff + gap version + stuff ... 62+@&67542+@ngap>

prompt.

> What if you do "sage -sh" and try to run "gap -r -b -p -T -o G
> /opt/sage/data//extcode/gap/sage.g" manually?  What error does it
> give?
> --Mike


-- 
Jason B. Hill
http://math.jasonbhill.com  |  jason.b.h...@colorado.edu

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Re: [sage-devel] build error in schroot+debootstrap

[Mike Hansen]

On Fri, Aug 12, 2011 at 2:54 PM, Jason B Hill  wrote:
> RuntimeError: Unable to start gap because the command 'gap -r -b -p -T
> -o G /opt/sage/data//extcode/gap/sage.g' failed.

What if you do "sage -sh" and try to run "gap -r -b -p -T -o G
/opt/sage/data//extcode/gap/sage.g" manually?  What error does it
give?
--Mike

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[sage-devel] build error in schroot+debootstrap

[Jason B Hill]

I'm wondering if anyone has any pointers on an error I'm getting.

In a schroot+debootstrap environment using Ubuntu 10.04 x86_64, I can
extract and run the binary of Sage 4.7 as root. I can also extract,
build, and run sage from source as root. Both of these fail in the
same way when I chown a built sage to my sageserver user, or when I
extract, build and run as sageserver. At the end of a build, I get:

  File "/opt/sage/local/lib/python2.6/site-packages/sage/interfaces/gap.py",
line 912, in _start
raise RuntimeError, msg
RuntimeError: Unable to start gap because the command 'gap -r -b -p -T
-o G /opt/sage/data//extcode/gap/sage.g' failed.

Some info:
- All of the dependencies for building sage are installed within my
10.04 chroot.
- Both the binary and the source build do function normally under the
root user in the chroot.
- The sageserver user is a fresh account (.e.g, no gaprc that could be
messing things up) and the schroot mounts are functioning fine
(allowing sage to read/write to /home/sageserver/.sage outside of the
chroot).

What am I missing?

-- 
Jason B. Hill
http://math.jasonbhill.com  |  jason.b.h...@colorado.edu

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[sage-devel] build error for sage 4.6.1 on OS X 10.5.8

[Jon Yard]

Hello,

I am having trouble building sage 4.6.1 on an iMac8,1 (2.4 GHz Intel Core 2
Duo) running OS X 10.5.8.  Below is the last relevant output from the
compilation.  Any help would be appreciated.

Thanks,
Jon


gcc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined
dynamic_lookup -single_module -multiply_defined suppress
-L/Users/jtyard/sage-4.6.1/local/lib/ -m64 -o grDevices.so chull.o devNull.o
devPicTeX.o devPS.o devQuartz.o init.o qdBitmap.o qdPDF.o qdCocoa.o
-framework AppKit -L../../../../lib -lR -dylib_file
libRblas.dylib:../../../../lib/libRblas.dylib -Wl,-framework
-Wl,CoreFoundation
ld warning: in qdCocoa.o, file is not of required architecture
make[8]: `Makedeps' is up to date.
mkdir ../../../../library/grDevices/libs
building package 'graphics'
mkdir ../../../library/graphics
mkdir ../../../library/graphics/R
mkdir ../../../library/graphics/po
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library
'/Users/jtyard/sage-4.6.1/spkg/build/r-2.10.1.p4/src/library/grDevices/libs/grDevices.so':
  
dlopen(/Users/jtyard/sage-4.6.1/spkg/build/r-2.10.1.p4/src/library/grDevices/libs/grDevices.so,
6): Symbol not found: _QuartzCocoa_DeviceCreate
  Referenced from:
/Users/jtyard/sage-4.6.1/spkg/build/r-2.10.1.p4/src/library/grDevices/libs/grDevices.so
  Expected in: dynamic lookup
Calls:  ... namespaceImport -> loadNamespace -> library.dynam ->
dyn.load
Execution halted
make[6]: *** [mklazy] Error 1
make[5]: *** [all] Error 2
make[4]: *** [R] Error 1
make[3]: *** [R] Error 1
make[2]: *** [R] Error 1
Error building R.

real 3m59.617s
user 2m54.940s
sys 0m39.710s
sage: An error occurred while installing r-2.10.1.p4
Please email sage-devel http://groups.google.com/group/sage-devel explaining
the problem and send the relevant part of of
/Users/jtyard/sage-4.6.1/install.log.  Describe your computer, operating
system, etc.

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Re: [sage-devel] build error if GREP_OPTIONS='--color=always'

[Jeroen Demeyer]

On 2010-11-07 11:50, rafaelf wrote:
> I don't know if this can be considered a bug: it seems that source
> files are generated via 'grep', but if the variable $GREP_OPTIONS
> contains '--color=always', these sources won't compile because of the
> extra characters which code the colors.
My personal opinion is that you should never set
GREP_OPTIONS=--color=always

I think many other programs (apart from Sage) would have problems with this.

Jeroen.

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Re: [sage-devel] build error if GREP_OPTIONS='--color=always'

[Jeroen Demeyer]

On 2010-11-07 13:33, Dr. David Kirkby wrote:
> On 11/ 7/10 10:50 AM, rafaelf wrote:
>> I don't know if this can be considered a bug: it seems that source
>> files are generated via 'grep', but if the variable $GREP_OPTIONS
>> contains '--color=always', these sources won't compile because of the
>> extra characters which code the colors.
>> So 'grep' in the build process should always be used with the option
>> '--color=never' to override the eventual 'always' from system-wide
>> options.
>>
> 
> What bit of code is this in?
> 
> Any use of grep with the options '--color' is non-portable, and should
> be removed.

Dave, I understand the poster's question is a different way:
If the *user* sets GREP_OPTIONS=--color=always, then some part of Sage
will not compile.

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Re: [sage-devel] build error if GREP_OPTIONS='--color=always'

[Dr. David Kirkby]

On 11/ 7/10 10:50 AM, rafaelf wrote:

I don't know if this can be considered a bug: it seems that source
files are generated via 'grep', but if the variable $GREP_OPTIONS
contains '--color=always', these sources won't compile because of the
extra characters which code the colors.
So 'grep' in the build process should always be used with the option
'--color=never' to override the eventual 'always' from system-wide
options.



What bit of code is this in?

Any use of grep with the options '--color' is non-portable, and should be 
removed.

Dave

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[sage-devel] build error if GREP_OPTIONS='--color=always'

[rafaelf]

I don't know if this can be considered a bug: it seems that source
files are generated via 'grep', but if the variable $GREP_OPTIONS
contains '--color=always', these sources won't compile because of the
extra characters which code the colors.
So 'grep' in the build process should always be used with the option
'--color=never' to override the eventual 'always' from system-wide
options.

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[sage-devel] Build error in sqlite-3.6.22 found by randomised testing.

[Dr. David Kirkby]

Following my attempts to build Sage, whilst inserting random delays in front of 
gcc/g++/gfortran, an error occured with sqlite-3.6.22.


This rather surprised me, as the sqlite team takes testing very seriously (more 
so than Sage),


http://www.sqlite.org/testing.html

with 647 times as much test code as actual source code for the database!


I'm begginging to wonder if building with delays to gcc is either a very good 
way to find bugs, or is a totally stupid way. I've built Singular 500 times 
without a build error now.



Dave



sqlite-3.6.22/.hgignore
Finished extraction

Host system
uname -a:
SunOS hawk 5.11 snv_134 i86pc i386 i86pc


CC Version
gcc -v
Using built-in specs.
COLLECT_GCC=/usr/local/gcc-4.5.0/bin/gcc
COLLECT_LTO_WRAPPER=/usr/local/gcc-4.5.0/libexec/gcc/i386-pc-solaris2.10/4.5.0/lto-wrapper
Target: i386-pc-solaris2.10
Configured with: ../gcc-4.5.0/configure --prefix=/usr/local/gcc-4.5.0 
--build=i386-pc-solaris2.10 --enable-languages=c,c++,fortran 
--with-gmp=/usr/local/gcc-4.5.0 --with-mpfr=/usr/local/gcc-4.5.0 --disable-nls 
--enable-checking=release --enable-werror=no --enable-multilib -with-system-zlib 
--enable-bootstrap --with-gnu-as --with-as=/usr/local/binutils-2.20/bin/as 
--without-gnu-ld --with-ld=/usr/ccs/bin/ld

Thread model: posix
gcc version 4.5.0 (GCC)

Code will be built with debugging information present. Set 'SAGE_DEBUG' to '0' 
if you don't want that.

Building sqlite using CC=gcc
  CCX=g++
  SAGE_FORTRAN=/usr/local/gcc-4.5.0-delayed/bin/gfortran
  F77=/usr/local/gcc-4.5.0-delayed/bin/gfortran
  FC=/usr/local/gcc-4.5.0-delayed/bin/gfortran
  CFLAGS= -g  -O2
  CXXFLAGS= -g  -O2
  FFLAGS= -g
  CPPFLAGS= -I 
/export/home/drkirkby/slow/sage-4.6.alpha1/local/include

checking for a BSD-compatible install... /usr/bin/ginstall -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make -j12 sets $(MAKE)... yes
checking for style of include used by make -j12... GNU
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking dependency style of gcc... gcc3
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... 64
checking for gcc... (cached) gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... (cached) yes
checking for gcc option to accept ISO C89... (cached) none needed
checking dependency style of gcc... (cached) gcc3
checking for ranlib... ranlib
checking build system type... i386-pc-solaris2.11
checking host system type... i386-pc-solaris2.11
checking for a sed that does not truncate output... /usr/bin/gsed
checking for grep that handles long lines and -e... /usr/bin/ggrep
checking for egrep... /usr/bin/ggrep -E
checking for ld used by gcc... ld
checking if the linker (ld) is GNU ld... no
checking for ld option to reload object files... -r
checking for BSD-compatible nm... /usr/bin/nm -p
checking whether ln -s works... yes
checking how to recognise dependent libraries... pass_all
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dlfcn.h usability... yes
checking dlfcn.h presence... yes
checking for dlfcn.h... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU Fortran 77 compiler... yes
checking whether /usr/local/gcc-4.5.0-delayed/bin/gfortran accepts -g... yes
checking the maximum length of command line arguments... 262144
checking command to parse /usr/bin/nm -p output from gcc object... ok
checking for objdir... .libs
checking for ar... ar
checking for ranlib... (cached) ranlib
checking for strip... strip
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC
checking if gcc PIC flag -fPIC works... yes
checking if gcc static flag -static works... no
checking 

[sage-devel] Build error: r-2.9.2

[Bryan Wilcox]

I am trying to build Sage 4.2.1 on a 32-bit 2.4 Ghz P4 running Ubuntu
9.04. The following error message is shown at completion:

--
Collecting examples for package ‘utils’
Running examples in package ‘utils’
Error: testing 'utils' failed
Execution halted
make[5]: *** [test-Examples-Base] Error 1
make[5]: Leaving directory
`/home/bryan/Software/sage-4.2.1/spkg/build/r-2.9.2/src/tests/Examples'
make[4]: *** [test-Examples] Error 2
make[4]: Leaving directory
`/home/bryan/Software/sage-4.2.1/spkg/build/r-2.9.2/src/tests'
make[3]: *** [test-all-basics] Error 1
make[3]: Leaving directory
`/home/bryan/Software/sage-4.2.1/spkg/build/r-2.9.2/src/tests'
make[2]: *** [check] Error 2
make[2]: Leaving directory
`/home/bryan/Software/sage-4.2.1/spkg/build/r-2.9.2/src'
Error while running the R testsuite ... exiting
*
Error testing package ** r-2.9.2 **
*
--

Please let me know if there is anything you would like me to try. I am
unfamiliar with the source, but willing to help.

Best,

Bryan

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[sage-devel] Build error: atlas-3.8.3.p0

[bparkis]

I'm on Ubuntu-8.04 on an i386 Macbook using KDE.  Kernel is 2.6.24-21-
server.

The install log is 45 megs, so here's just the last stage where it
failed:

   STAGE 2-4-5: GEMV TUNE
make -f Makefile INSTALL_LOG/cMVRES pre=c 2>&1 | ./xatlas_tee
INSTALL_LOG/cMVTUNE.LOG
make[3]: *** [build] Error 255
make[3]: Leaving directory `/home/bparkis/downloads/sage-3.4/spkg/
build/atlas-3.8.3.p0/ATLAS-build'
make[2]: *** [build] Error 2
make[2]: Leaving directory `/home/bparkis/downloads/sage-3.4/spkg/
build/atlas-3.8.3.p0/ATLAS-build'
Failed to build ATLAS.
ATLAS failed to build for the 1-th time, possibly because of a
loaded system, so we will automatically try again up to 4 more times.
Waiting 13 minutes...
ATLAS failed to build for the 2-th time, possibly because of a
loaded system, so we will automatically try again up to 3 more times.
Waiting 9 minutes...
ATLAS failed to build for the 3-th time, possibly because of a
loaded system, so we will automatically try again up to 2 more times.
Waiting 5 minutes...
ATLAS failed to build for the 4-th time, possibly because of a
loaded system, so we will automatically try again up to 1 more times.
Waiting 10 minutes...
Too many failures to build atlas.  Giving up!

real661m12.872s
user600m18.360s
sys 17m57.330s
sage: An error occurred while installing atlas-3.8.3.p0
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /home/bparkis/downloads/sage-3.4/install.log.  Describe your
computer, operating system, etc.
If you want to try to fix the problem, yourself *don't* just cd to
/home/bparkis/downloads/sage-3.4/spkg/build/atlas-3.8.3.p0 and type
'make'.
Instead type "/home/bparkis/downloads/sage-3.4/sage -sh"
in order to set all environment variables correctly, then cd to
/home/bparkis/downloads/sage-3.4/spkg/build/atlas-3.8.3.p0
(When you are done debugging, you can type "exit" to leave the
subshell.)
make[1]: *** [installed/atlas-3.8.3.p0] Error 1
make[1]: Leaving directory `/home/bparkis/downloads/sage-3.4/spkg'
Command exited with non-zero status 2
38237.40user 1419.56system 11:45:57elapsed 93%CPU (0avgtext+0avgdata
0maxresident)k
138712inputs+6830704outputs (787major+227570476minor)pagefaults 0swaps
python: can't open file '/home/bparkis/downloads/sage-3.4/devel/sage/
doc/common/builder.py': [Errno 2] No such file or directory

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[sage-devel] Build error on SiCortex, mixing n32 and 62 ABIs

[mcelis]

Hi,

I am trying to build SAGE on a SiCortex machine with MIPS processors
running Linux Gentoo Base System release 1.12.12.

The build/install for libpari-gmp failed (results below). I believe it
is because -lgmp gets built using -n32 while libpari-gmp is being
built with the default n64. Is there a way to control which ABI the
build for the different packages is selected?

GCC Version
gcc -v
Using built-in specs.
Target: mips64el-gentoo-linux-gnu
Configured with: /opt/sicortex/rootfs/build/var/tmp/portage/sys-devel/
gcc-4.1.2/work/gcc-4.1.2/configure --prefix=/usr --bindir=/usr/
mips64el-gentoo-linux-gnu/gcc-bin/4.1.2 --includedir=/usr/lib/gcc/
mips64el-gentoo-linux-gnu/4.1.2/include --datadir=/usr/share/gcc-data/
mips64el-gentoo-linux-gnu/4.1.2 --mandir=/usr/share/gcc-data/mips64el-
gentoo-linux-gnu/4.1.2/man --infodir=/usr/share/gcc-data/mips64el-
gentoo-linux-gnu/4.1.2/info --with-gxx-include-dir=/usr/lib/gcc/
mips64el-gentoo-linux-gnu/4.1.2/include/g++-v4 --host=mips64el-gentoo-
linux-gnu --target=mips64el-gentoo-linux-gnu --build=x86_64-pc-linux-
gnu --disable-altivec --disable-nls --with-system-zlib --disable-
checking --disable-werror --enable-secureplt --disable-libunwind-
exceptions --enable-multilib --enable-libmudflap --disable-libssp --
disable-libgcj --with-abi=64 --with-arch=5kf --enable-languages=c,c+
+,fortran --enable-shared --enable-threads=posix --enable-__cxa_atexit
--enable-clocale=gnu
Thread model: posix
gcc version 4.1.2 (Gentoo 4.1.2)


gcc  -o libpari-gmp.so.2.3.3 -shared  -O3 -Wall -fno-strict-aliasing -
fomit-frame-pointer -Wl,-shared,-soname=libpari-gmp.so.2 mp.o
mpinl.o Flx.o Qfb.o RgX.o alglin1.o alglin2.o arith1.o arith2.o
base1.o base2.o base3.o base4.o base5.o bibli1.o bibli2.o buch1.o
buch2.o buch3.o buch4.o galconj.o gen1.o gen2.o gen3.o ifactor1.o
perm.o polarit1.o polarit2.o polarit3.o rootpol.o subcyclo.o
subgroup.o trans1.o trans2.o trans3.o anal.o compat.o default.o
errmsg.o es.o init.o intnum.o members.o sumiter.o aprcl.o elldata.o
elliptic.o galois.o groupid.o kummer.o mpqs.o nffactor.o part.o
stark.o subfield.o thue.o -lc -ldl -lm -L/home/mcelis/sage/sage-3.1.4/
local/lib -lgmp
/home/mcelis/sage/sage-3.1.4/local/lib/libgmp.so: could not read
symbols: File in wrong format
collect2: ld returned 1 exit status
make[3]: *** [libpari-gmp.so.2.3.3] Error 1
make[3]: Leaving directory `/.root0/net/home/mcelis/sage/sage-3.1.4/
spkg/build/pari-2.3.3.p0/src/Olinux-mips64'
make[2]: *** [gp] Error 2
make[2]: Leaving directory `/.root0/net/home/mcelis/sage/sage-3.1.4/
spkg/build/pari-2.3.3.p0/src'
Error building GP

real16m58.016s
user15m15.507s
sys 0m25.501s
sage: An error occurred while installing pari-2.3.3.p0
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /home/mcelis/sage/sage-3.1.4/install.log.  Describe your computer,
operating system, etc.
If you want to try to fix the problem, yourself *don't* just cd to
/home/mcelis/sage/sage-3.1.4/spkg/build/pari-2.3.3.p0 and type 'make'.
Instead type "/home/mcelis/sage/sage-3.1.4/sage -sh"
in order to set all environment variables correctly, then cd to
/home/mcelis/sage/sage-3.1.4/spkg/build/pari-2.3.3.p0
(When you are done debugging, you can type "exit" to leave the
subshell.)
make[1]: *** [installed/pari-2.3.3.p0] Error 1
make[1]: Leaving directory `/.root0/net/home/mcelis/sage/sage-3.1.4/
spkg'

Thank you
Mimi

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[sage-devel] Build Error

[Walt]

Just got this build error that told me to post it here:

mpn_extras.o:mpn_extras.c:(.text+0x2630): first defined here
collect2: ld returned 1 exit status
make[2]: *** [libflint.so] Error 1
make[2]: Leaving directory `/home/zarathustra/Download/sage-3.0.alpha3/
spkg/build/flint-1.06.p2/src'
Error building flint shared library.

real0m23.087s
user0m22.184s
sys 0m0.559s
sage: An error occurred while installing flint-1.06.p2
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /home/zarathustra/Download/sage-3.0.alpha3/install.log.  Describe
your computer, operating system, etc.
If you want to try to fix the problem, yourself *don't* just cd to
/home/zarathustra/Download/sage-3.0.alpha3/spkg/build/flint-1.06.p2
and type 'make'.
Instead type "/home/zarathustra/Download/sage-3.0.alpha3/sage -sh"
in order to set all environment variables correctly, then cd to
/home/zarathustra/Download/sage-3.0.alpha3/spkg/build/flint-1.06.p2
(When you are done debugging, you can type "exit" to leave the
subshell.)
make[1]: *** [installed/flint-1.06.p2] Error 1
make[1]: Leaving directory `/home/zarathustra/Download/sage-3.0.alpha3/
spkg'

real19m40.074s
user17m33.744s
sys 1m27.617s


Any advice?
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[sage-devel] build error

[Lukas Diduch]

- build failed for libiml @ linking stage

replacing '/local/home/ldemo/software/sage-2.8.3.rc2/local/lib/libgmp.so' with
'-lgmp' would solve the problem.

i guess the libtool script is responsible for the error. solving this by hand
however is hard because make (in the root tree) does rebuild the local
Makefile, which results in running into the same problem.

- system

Linux 2.6.15-1.2054_FC5 #1 SMP Tue Mar 14 15:57:06 EST 2006 ppc64 ppc64 ppc64 
GNU/Linux
(mac pro quadcore with fedora core 5 installed)

- versions 

sage-2.8.3.rc2
sage-2.8.2
both throw the same error while building


greetings
L

build log pieces:
--

Finished extraction

Host system
uname -a:
Linux xxx 2.6.15-1.2054_FC5 #1 SMP Tue Mar 14 15:57:06 EST 2006 
ppc64 ppc64 ppc64 GNU/Linux


GCC Version
gcc -v
Using built-in specs.
Target: ppc64-redhat-linux
Configured with: ../configure --prefix=/usr --mandir=/usr/share/man 
--infodir=/usr/share/info --enable-shared --enable-threads=posix 
--enable-checking=release --with-system-zlib --enable-__cxa_atexit 
--disable-libunwind-exceptions --enable-libgcj-multifile 
--enable-languages=c,c++,objc,obj-c++,java,fortran --enable-java-awt=gtk 
--disable-dssi --with-java-home=/usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre 
--enable-secureplt --with-long-double-128 --host=ppc64-redhat-linux 
--build=ppc64-redhat-linux --target=ppc64-redhat-linux --with-cpu=default32
Thread model: posix
gcc version 4.1.0 20060304 (Red Hat 4.1.0-3)

checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes




Default checking path = /usr /usr/local
checking for GMP >= 3.1.1... found
checking whether GMP is 4.0 or greater... yes
checking for ATLAS >= 3.0... configure: creating ./config.status
config.status: creating Makefile
config.status: creating config/Makefile
config.status: creating repl/Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating examples/Makefile
config.status: creating tests/Makefile
config.status: creating config.h
config.status: executing depfiles commands

Configuration:

Source code location:   .
Compiler:   gcc
Compiler flags: -I. -g -O2
Linker flags:-lm
Host System Type:   powerpc64-redhat-linux-gnu
Install path:   /local/home/ldemo/software/sage-2.8.3.rc2/local

See config.h for further configuration information.

make[2]: Entering directory 
`/local/home/ldemo/software/sage-2.8.3.rc2/spkg/build/iml-1.0.1.p6/src'
make  all-recursive
make[3]: Entering directory 
`/local/home/ldemo/software/sage-2.8.3.rc2/spkg/build/iml-1.0.1.p6/src'
Making all in repl
make[4]: Entering directory 
`/local/home/ldemo/software/sage-2.8.3.rc2/spkg/build/iml-1.0.1.p6/src/repl'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory 
`/local/home/ldemo/software/sage-2.8.3.rc2/spkg/build/iml-1.0.1.p6/src/repl'
Making all in config
make[4]: Entering directory 
`/local/home/ldemo/software/sage-2.8.3.rc2/spkg/build/iml-1.0.1.p6/src/config'
make[4]: Nothing to be done for `all'.
make[4]: Leaving directory 
`/local/home/ldemo/software/sage-2.8.3.rc2/spkg/build/iml-1.0.1.p6/src/config'
Making all in src
make[4]: Entering directory 
`/local/home/ldemo/software/sage-2.8.3.rc2/spkg/build/iml-1.0.1.p6/src/src'
if /bin/sh ../libtool --tag=CC --mode=compile gcc -DHAVE_CONFIG_H -I. -I. -I..  
  -I/local/home/ldemo/software/sage-2.8.3.rc2/local/include  -I. -g -O2 -MT 
libiml_la-basisop.lo -MD -MP -MF ".deps/libiml_la-basisop.Tpo" -c -o 
libiml_la-basisop.lo `test -f 'basisop.c' || echo './'`basisop.c; \
then mv -f ".deps/libiml_la-basisop.Tpo" ".deps/libiml_la-basisop.Plo"; else rm 
-f ".deps/libiml_la-basisop.Tpo"; exit 1; fi
mkdir .libs
gcc -DHAVE_CONFIG_H -I. -I. -I.. 
-I/local/home/ldemo/software/sage-2.8.3.rc2/local/include -I. -g -O2 -MT 
libiml_la-basisop.lo -MD -MP -MF .deps/libiml_la-basisop.Tpo -c basisop.c  
-fPIC -DPIC -o .libs/libiml_la-basisop.o
gcc -DHAVE_CONFIG_H -I. -I. -I.. 
-I/local/home/ldemo/software/sage-2.8.3.rc2/local/include -I. -g -O2 -MT 
libiml_la-basisop.lo -MD -MP -MF .deps/libiml_la-basisop.Tpo -c basisop.c -o 
libiml_la-basisop.o >/dev/nu

[sage-devel] Build error in matrix_integer_dense.pyx

[Robert Miller]

Getting the following error when building the latest version of SAGE:

robert-millers-powerbook-g4-12:/Volumes/DATA/sage-1.7 robert$ sage -br

--
sage: Building and installing modified SAGE library files.

pyrexc --embed-positions -I/Volumes/DATA/sage-1.7/devel/sage-main
sage/matrix/matrix_integer_dense.pyx

Error converting Pyrex file to C:

...
#moduli = [ start_prime ]
residues = [ left._mod_int(start_prime) *
right._mod_int(start_prime) ]
cur_prime = start_prime
while product < height:
cur_prime = next_prime(cur_prime)
product *= cur_prime
^


/Volumes/DATA/sage-1.7/devel/sage-main/sage/matrix/matrix_integer_dense.pyx:614:21:
Expected an identifier or literal
sage: Error running pyrexc.
sage: There was an error installing modified sage library code.


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