Re: [sage-devel] Sage compilation

[Dima Pasechnik]

texinfo is not necessary.
Just try

make build



On Sun, 12 Jun 2022, 15:48 David Kohel,  wrote:

> This still gave the same error.  If I instead deactivate conda, I get
> further, but
> with the homebrew installation it fails to find texinfo:
>
> configure:
>
> hint: installing the following system packages, if not
> already present, may provide additional optional features:
>
>   $ brew install texinfo
>
> Homebrew can issue suggestions regarding keg-only packages.
> The following command is to automatically apply these suggestions
> for packages relevant for Sage to make them available for the build.
> Run it once to apply the suggestions for the current session.
> Add it to your shell profile to apply them for all future sessions.
>
>   $ source /usr/local/sage-9.6/.homebrew-build-env
>
> configure:
>
> hint: After installation, re-run configure using:
>
>   $ ./config.status --recheck && ./config.status
>
> Following these instructions it verifies that the texinfo is installed,
> but I get the
> same failure from configuration.
>
> Is there any chance that this would be easier to debug?  The full log is
> attached.
>
> --David
>
> On Sunday, June 12, 2022 at 3:06:45 PM UTC+2 dim...@gmail.com wrote:
>
>> On Sun, Jun 12, 2022 at 1:23 PM David Kohel 
>> wrote:
>> >
>> > I'm been unable to compile Sage on my MacOS laptop (Monterrey, x86
>> intel)
>> >
>> > I've tried installing all homebrew packages requested, but it tends to
>> > still not
>> > find them (path problem?). I switched to using conda, following the
>> > directions
>> > here:
>> >
>> > https://doc.sagemath.org/html/en/installation/conda.html
>> >
>> > but it fails with the error message below (another path problem?). The
>> > config
>> > log file is attached.
>> >
>> > Any suggestions would be appreciated.
>> >
>> > --David Kohel
>> >
>> > Checking whether SageMath should install SPKG gmp...
>> > checking gmp.h usability... yes
>> > checking gmp.h presence... no
>> > configure: WARNING: gmp.h: accepted by the compiler, rejected by the
>> > preprocessor!
>> > configure: WARNING: gmp.h: proceeding with the compiler's result
>> > checking for gmp.h... yes
>> > checking gmpxx.h usability... yes
>> > checking gmpxx.h presence... no
>> > configure: WARNING: gmpxx.h: accepted by the compiler, rejected by the
>> > preprocessor!
>> > configure: WARNING: gmpxx.h: proceeding with the compiler's result
>> > checking for gmpxx.h... yes
>> > checking for library containing __gmpq_cmp_z... -lgmp
>> > configure: will use system package and not install SPKG gmp
>> > checking absolute name of ... checking for gmp.h... (cached) yes
>> >
>> > configure: error: failed to find absolute path to gmp.h despite it
>> being
>> > reported found
>> >
>> this is due to the test in build/pkgs/gmp/spkg-configure.m4
>>
>> AX_ABSOLUTE_HEADER([gmp.h])
>> if test x$gl_cv_absolute_gmp_h = x; then
>> AC_MSG_ERROR(m4_normalize([
>> failed to find absolute path to gmp.h despite it being reported
>> found
>> ]))
>> fi
>> AC_SUBST(SAGE_GMP_INCLUDE, [`AS_DIRNAME($gl_cv_absolute_gmp_h)`])
>>
>> Replace this fragment with
>>
>> AC_SUBST(SAGE_GMP_INCLUDE, [' '])
>>
>> and re-run ./bootstrap
>>
>> this will disable this check - I also assume that any package that
>> potentially needs
>> the correct value of SAGE_GMP_INCLUDE actually comes from Conda anyway,
>> and so
>> this value, the absolute path to GMP include headers, is not relevant;
>> it can also be replaced with the value in question, say, /foo/bar, if
>> needed, by using instead
>>
>> AC_SUBST(SAGE_GMP_INCLUDE, ['/foo/bar/'])
>>
>>
>>
>>
>>
>>
>> > --
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>> Groups "sage-devel" group.
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>> an email to sage-devel+...@googlegroups.com.
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>> https://groups.google.com/d/msgid/sage-devel/86561d45-63e9-69fb-9361-4142fa731a9d%40univ-amu.fr.
>>
>>
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> .
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Re: [sage-devel] Sage compilation

[Dima Pasechnik]

On Sun, Jun 12, 2022 at 1:23 PM David Kohel  wrote:
>
> I'm been unable to compile Sage on my MacOS laptop (Monterrey, x86 intel)
>
> I've tried installing all homebrew packages requested, but it tends to
> still not
> find them (path problem?).  I switched to using conda, following the
> directions
> here:
>
> https://doc.sagemath.org/html/en/installation/conda.html
>
> but it fails with the error message below (another path problem?). The
> config
> log file is attached.
>
> Any suggestions would be appreciated.
>
> --David Kohel
>
> Checking whether SageMath should install SPKG gmp...
> checking gmp.h usability... yes
> checking gmp.h presence... no
> configure: WARNING: gmp.h: accepted by the compiler, rejected by the
> preprocessor!
> configure: WARNING: gmp.h: proceeding with the compiler's result
> checking for gmp.h... yes
> checking gmpxx.h usability... yes
> checking gmpxx.h presence... no
> configure: WARNING: gmpxx.h: accepted by the compiler, rejected by the
> preprocessor!
> configure: WARNING: gmpxx.h: proceeding with the compiler's result
> checking for gmpxx.h... yes
> checking for library containing __gmpq_cmp_z... -lgmp
> configure: will use system package and not install SPKG gmp
> checking absolute name of ... checking for gmp.h... (cached) yes
>
> configure: error: failed to find absolute path to gmp.h despite it being
> reported found
>
this is due to the test in build/pkgs/gmp/spkg-configure.m4

AX_ABSOLUTE_HEADER([gmp.h])
if test x$gl_cv_absolute_gmp_h = x; then
AC_MSG_ERROR(m4_normalize([
failed to find absolute path to gmp.h despite it being reported
found
]))
fi
AC_SUBST(SAGE_GMP_INCLUDE, [`AS_DIRNAME($gl_cv_absolute_gmp_h)`])

Replace this fragment with

AC_SUBST(SAGE_GMP_INCLUDE, [' '])

and re-run ./bootstrap

this will disable this check - I also assume that any package that
potentially needs
the correct value of SAGE_GMP_INCLUDE actually comes from Conda anyway, and so
this value, the absolute path to GMP include headers, is not relevant;
it can also be replaced with the value in question, say, /foo/bar,  if
needed, by using instead

   AC_SUBST(SAGE_GMP_INCLUDE, ['/foo/bar/'])






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[sage-devel] Sage compilation

[David Kohel]

I'm been unable to compile Sage on my MacOS laptop (Monterrey, x86 intel)

I've tried installing all homebrew packages requested, but it tends to 
still not
find them (path problem?).  I switched to using conda, following the 
directions

here:

https://doc.sagemath.org/html/en/installation/conda.html

but it fails with the error message below (another path problem?). The 
config

log file is attached.

Any suggestions would be appreciated.

--David Kohel

Checking whether SageMath should install SPKG gmp...
checking gmp.h usability... yes
checking gmp.h presence... no
configure: WARNING: gmp.h: accepted by the compiler, rejected by the 
preprocessor!

configure: WARNING: gmp.h: proceeding with the compiler's result
checking for gmp.h... yes
checking gmpxx.h usability... yes
checking gmpxx.h presence... no
configure: WARNING: gmpxx.h: accepted by the compiler, rejected by the 
preprocessor!

configure: WARNING: gmpxx.h: proceeding with the compiler's result
checking for gmpxx.h... yes
checking for library containing __gmpq_cmp_z... -lgmp
configure: will use system package and not install SPKG gmp
checking absolute name of ... checking for gmp.h... (cached) yes

configure: error: failed to find absolute path to gmp.h despite it being 
reported found


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This file contains any messages produced by compilers while
running configure, to aid debugging if configure makes a mistake.

It was created by Sage configure 9.7.beta1, which was
generated by GNU Autoconf 2.69.  Invocation command line was

  $ ./configure --prefix=/Applications/anaconda3/envs/sage-build

## - ##
## Platform. ##
## - ##

hostname = bunyip.home
uname -m = x86_64
uname -r = 21.5.0
uname -s = Darwin
uname -v = Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; 
root:xnu-8020.121.3~4/RELEASE_X86_64

/usr/bin/uname -p = i386
/bin/uname -X = unknown

/bin/arch  = unknown
/usr/bin/arch -k   = unknown
/usr/convex/getsysinfo = unknown
/usr/bin/hostinfo  = Mach kernel version:
 Darwin Kernel Version 21.5.0: Tue Apr 26 21:08:22 PDT 2022; 
root:xnu-8020.121.3~4/RELEASE_X86_64
Kernel configured for up to 4 processors.
2 processors are physically available.
4 processors are logically available.
Processor type: x86_64h (Intel x86-64h Haswell)
Processors active: 0 1 2 3
Primary memory available: 16.00 gigabytes
Default processor set: 511 tasks, 2100 threads, 4 processors
Load average: 13.69, Mach factor: 0.29
/bin/machine   = unknown
/usr/bin/oslevel   = unknown
/bin/universe  = unknown

PATH: /Applications/anaconda3/envs/sage-build/bin
PATH: /Applications/anaconda3/condabin
PATH: /usr/local/opt/texinfo/bin
PATH: /Library/Frameworks/Python.framework/Versions/3.9/bin
PATH: /Users/kohel/.nvm/versions/node/v8.17.0/bin
PATH: /usr/local/opt
PATH: /Library/Frameworks/Python.framework/Versions/2.7/bin
PATH: /usr/local/texlive/2019/bin/x86_64-darwin
PATH: /usr/local/bin
PATH: /usr/local/bin
PATH: /usr/bin
PATH: /bin
PATH: /usr/sbin
PATH: /sbin
PATH: /Library/TeX/texbin
PATH: /usr/local/go/bin
PATH: /Library/Apple/usr/bin
PATH: /Applications/Magma
PATH: /Users/kohel/bin
PATH: /usr/local/go/bin


## --- ##
## Core tests. ##
## --- ##

configure:4334: checking for a BSD-compatible install
configure:4402: result: /usr/bin/install -c
configure:4413: checking whether build environment is sane
configure:4468: result: yes
configure:4614: checking for a thread-safe mkdir -p
configure:4653: result: config/install-sh -c -d
configure:4660: checking for gawk
configure:4690: result: no
configure:4660: checking for mawk
configure:4690: result: no
configure:4660: checking for nawk
configure:4690: result: no
configure:4660: checking for awk
configure:4676: found /usr/bin/awk
configure:4687: result: awk
configure:4698: checking whether make sets $(MAKE)
configure:4720: result: yes
configure:4749: checking whether make supports nested variables
configure:4766: result: yes
configure:4909: checking whether to enable maintainer-specific portions of 
Makefiles
configure:4918: result: yes
configure:4938: checking whether make supports the include directive
configure:4953: make -f confmf.GNU && cat confinc.out
this is the am__doit target
configure:4956: $? = 0
configure:4975: result: yes (GNU style)
configure:5005: checking for x86_64-apple-darwin13.4.0-gcc
configure:5032: result: x86_64-apple-darwin13.4.0-clang
configure:5301: checking for C compiler version
configure:5310: x86_64-apple-darwin13.4.0-clang --version >&5
clang version 13.0.1
Target: x86_64-apple-darwin13.4.0
Thread model: posix
InstalledDir: 

Re: [sage-devel] Sage Compilation Error

[E. Madison Bray]

On Sun, Feb 24, 2019 at 8:22 PM Paul Clarke  wrote:
>
> Ok, good to know. Where can I find that beta? I have cloned the github 
> repository at git://github.com/sagemath/sage.git
> and it looks like the most recent version on the develop branch is 8.7.beta5

It's not necessary.  Just install your Linux distribution's `gfortran`
package.  Unless it's older than, say, version 4.8, it will work.
There's no reason to compile it just for Sage.


> On Sunday, February 24, 2019 at 1:02:30 PM UTC-6, vdelecroix wrote:
>>
>> This was
>>
>> https://trac.sagemath.org/ticket/27016
>>
>> which is indeed merged in 8.7.beta6
>>
>> Le 24/02/2019 à 20:00, Dima Pasechnik a écrit :
>> > This looks like a known bug, fixed in the latest beta I believe.
>> >
>> > On Sun, 24 Feb 2019 19:42 Paul Clarke,  wrote:
>> >
>> >> Hello,
>> >> Sage failed during compilation of the gfortran component. It appears that
>> >> the files were compiled successfully, but there was an error when copying
>> >> them to their final destination.
>> >>
>> >> Here is the error message:
>> >>
>> >> [gfortran-7.2.0] Copying package files from temporary location
>> >> /media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst 
>> >> to
>> >> /media/paul/str/source/sage/local
>> >> [gfortran-7.2.0] cp: cannot overwrite non-directory
>> >> '/media/paul/str/source/sage/local/./lib64' with directory
>> >> '/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst/media/paul/str/source/sage/local/./lib64'
>> >> [gfortran-7.2.0]
>> >> 
>> >> [gfortran-7.2.0] Error copying files for gfortran-7.2.0.
>> >> [gfortran-7.2.0]
>> >> 
>> >> [gfortran-7.2.0] Please email sage-devel (
>> >> http://groups.google.com/group/sage-devel)
>> >> [gfortran-7.2.0] explaining the problem and including the log file
>> >> [gfortran-7.2.0]   
>> >> /media/paul/str/source/sage/logs/pkgs/gfortran-7.2.0.log
>> >> [gfortran-7.2.0] Describe your computer, operating system, etc.
>> >> [gfortran-7.2.0]
>> >> 
>> >> Makefile:2124: recipe for target
>> >> '/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0'
>> >> failed
>> >> make[3]: ***
>> >> [/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0]
>> >> Error 1
>> >> make[3]: Leaving directory '/media/paul/str/source/sage/build/make'
>> >> Makefile:1801: recipe for target 'all-start' failed
>> >> make[2]: *** [all-start] Error 2
>> >> make[2]: Leaving directory '/media/paul/str/source/sage/build/make'
>> >>
>> >> real35m24.461s
>> >> user28m44.864s
>> >> sys3m53.390s
>> >> ***
>> >>
>> >> My computer is a chromebook pixel 2015 running linux mint 18.2. Linux
>> >> kernel 4.15.0-lowlatency. The sage source directory is
>> >> /media/paul/str/source/sage (it's an external sd card). The log file is
>> >> around 12 MB(ending with the error message I copied) so I have created a
>> >> Google drive link to it:
>> >>
>> >> https://drive.google.com/file/d/1uhm0WZ2eZ8N-Dj7RQ8sMSFjz_ourK1I_/view?usp=sharing.
>> >>
>> >>
>> >> Can anyone tell what is going wrong here? Is this a known bug? Thank you
>> >> for your help,
>> >> Paul
>> >>
>> >> --
>> >> 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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>> >> Visit this group at https://groups.google.com/group/sage-devel.
>> >> For more options, visit https://groups.google.com/d/optout.
>> >>
>> >
>
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Re: [sage-devel] Sage Compilation Error

[Vincent Delecroix]

A typo: beta6 -> beta5

You have the good version

Le 24/02/2019 à 20:22, Paul Clarke a écrit :

Ok, good to know. Where can I find that beta? I have cloned the github
repository at git://github.com/sagemath/sage.git
and it looks like the most recent version on the develop branch is 8.7.beta5

On Sunday, February 24, 2019 at 1:02:30 PM UTC-6, vdelecroix wrote:


This was

https://trac.sagemath.org/ticket/27016

which is indeed merged in 8.7.beta6

Le 24/02/2019 à 20:00, Dima Pasechnik a écrit :

This looks like a known bug, fixed in the latest beta I believe.

On Sun, 24 Feb 2019 19:42 Paul Clarke, 
> wrote:



Hello,
Sage failed during compilation of the gfortran component. It appears

that

the files were compiled successfully, but there was an error when

copying

them to their final destination.

Here is the error message:

[gfortran-7.2.0] Copying package files from temporary location


/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst to

/media/paul/str/source/sage/local
[gfortran-7.2.0] cp: cannot overwrite non-directory
'/media/paul/str/source/sage/local/./lib64' with directory


'/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst/media/paul/str/source/sage/local/./lib64'


[gfortran-7.2.0]




[gfortran-7.2.0] Error copying files for gfortran-7.2.0.
[gfortran-7.2.0]




[gfortran-7.2.0] Please email sage-devel (
http://groups.google.com/group/sage-devel)
[gfortran-7.2.0] explaining the problem and including the log file
[gfortran-7.2.0]

/media/paul/str/source/sage/logs/pkgs/gfortran-7.2.0.log

[gfortran-7.2.0] Describe your computer, operating system, etc.
[gfortran-7.2.0]




Makefile:2124: recipe for target


'/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0'

failed
make[3]: ***


[/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0]

Error 1
make[3]: Leaving directory '/media/paul/str/source/sage/build/make'
Makefile:1801: recipe for target 'all-start' failed
make[2]: *** [all-start] Error 2
make[2]: Leaving directory '/media/paul/str/source/sage/build/make'

real35m24.461s
user28m44.864s
sys3m53.390s
***

My computer is a chromebook pixel 2015 running linux mint 18.2. Linux
kernel 4.15.0-lowlatency. The sage source directory is
/media/paul/str/source/sage (it's an external sd card). The log file is
around 12 MB(ending with the error message I copied) so I have created

a

Google drive link to it:



https://drive.google.com/file/d/1uhm0WZ2eZ8N-Dj7RQ8sMSFjz_ourK1I_/view?usp=sharing.




Can anyone tell what is going wrong here? Is this a known bug? Thank

you

for your help,
Paul

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Re: [sage-devel] Sage Compilation Error

[Paul Clarke]

Ok, good to know. Where can I find that beta? I have cloned the github 
repository at git://github.com/sagemath/sage.git 
and it looks like the most recent version on the develop branch is 8.7.beta5

On Sunday, February 24, 2019 at 1:02:30 PM UTC-6, vdelecroix wrote:
>
> This was 
>
> https://trac.sagemath.org/ticket/27016 
>
> which is indeed merged in 8.7.beta6 
>
> Le 24/02/2019 à 20:00, Dima Pasechnik a écrit : 
> > This looks like a known bug, fixed in the latest beta I believe. 
> > 
> > On Sun, 24 Feb 2019 19:42 Paul Clarke,  > wrote: 
> > 
> >> Hello, 
> >> Sage failed during compilation of the gfortran component. It appears 
> that 
> >> the files were compiled successfully, but there was an error when 
> copying 
> >> them to their final destination. 
> >> 
> >> Here is the error message: 
> >> 
> >> [gfortran-7.2.0] Copying package files from temporary location 
> >> 
> /media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst to 
> >> /media/paul/str/source/sage/local 
> >> [gfortran-7.2.0] cp: cannot overwrite non-directory 
> >> '/media/paul/str/source/sage/local/./lib64' with directory 
> >> 
> '/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst/media/paul/str/source/sage/local/./lib64'
>  
>
> >> [gfortran-7.2.0] 
> >> 
>  
> >> [gfortran-7.2.0] Error copying files for gfortran-7.2.0. 
> >> [gfortran-7.2.0] 
> >> 
>  
> >> [gfortran-7.2.0] Please email sage-devel ( 
> >> http://groups.google.com/group/sage-devel) 
> >> [gfortran-7.2.0] explaining the problem and including the log file 
> >> [gfortran-7.2.0]   
> /media/paul/str/source/sage/logs/pkgs/gfortran-7.2.0.log 
> >> [gfortran-7.2.0] Describe your computer, operating system, etc. 
> >> [gfortran-7.2.0] 
> >> 
>  
> >> Makefile:2124: recipe for target 
> >> 
> '/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0' 
> >> failed 
> >> make[3]: *** 
> >> 
> [/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0] 
> >> Error 1 
> >> make[3]: Leaving directory '/media/paul/str/source/sage/build/make' 
> >> Makefile:1801: recipe for target 'all-start' failed 
> >> make[2]: *** [all-start] Error 2 
> >> make[2]: Leaving directory '/media/paul/str/source/sage/build/make' 
> >> 
> >> real35m24.461s 
> >> user28m44.864s 
> >> sys3m53.390s 
> >> *** 
> >> 
> >> My computer is a chromebook pixel 2015 running linux mint 18.2. Linux 
> >> kernel 4.15.0-lowlatency. The sage source directory is 
> >> /media/paul/str/source/sage (it's an external sd card). The log file is 
> >> around 12 MB(ending with the error message I copied) so I have created 
> a 
> >> Google drive link to it: 
> >> 
> >> 
> https://drive.google.com/file/d/1uhm0WZ2eZ8N-Dj7RQ8sMSFjz_ourK1I_/view?usp=sharing.
>  
>
> >> 
> >> 
> >> Can anyone tell what is going wrong here? Is this a known bug? Thank 
> you 
> >> for your help, 
> >> Paul 
> >> 
> >> -- 
> >> 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 https://groups.google.com/group/sage-devel. 
> >> For more options, visit https://groups.google.com/d/optout. 
> >> 
> > 
>

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Re: [sage-devel] Sage Compilation Error

[Vincent Delecroix]

This was

https://trac.sagemath.org/ticket/27016

which is indeed merged in 8.7.beta6

Le 24/02/2019 à 20:00, Dima Pasechnik a écrit :

This looks like a known bug, fixed in the latest beta I believe.

On Sun, 24 Feb 2019 19:42 Paul Clarke,  wrote:


Hello,
Sage failed during compilation of the gfortran component. It appears that
the files were compiled successfully, but there was an error when copying
them to their final destination.

Here is the error message:

[gfortran-7.2.0] Copying package files from temporary location
/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst to
/media/paul/str/source/sage/local
[gfortran-7.2.0] cp: cannot overwrite non-directory
'/media/paul/str/source/sage/local/./lib64' with directory
'/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst/media/paul/str/source/sage/local/./lib64'
[gfortran-7.2.0]

[gfortran-7.2.0] Error copying files for gfortran-7.2.0.
[gfortran-7.2.0]

[gfortran-7.2.0] Please email sage-devel (
http://groups.google.com/group/sage-devel)
[gfortran-7.2.0] explaining the problem and including the log file
[gfortran-7.2.0]   /media/paul/str/source/sage/logs/pkgs/gfortran-7.2.0.log
[gfortran-7.2.0] Describe your computer, operating system, etc.
[gfortran-7.2.0]

Makefile:2124: recipe for target
'/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0'
failed
make[3]: ***
[/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0]
Error 1
make[3]: Leaving directory '/media/paul/str/source/sage/build/make'
Makefile:1801: recipe for target 'all-start' failed
make[2]: *** [all-start] Error 2
make[2]: Leaving directory '/media/paul/str/source/sage/build/make'

real35m24.461s
user28m44.864s
sys3m53.390s
***

My computer is a chromebook pixel 2015 running linux mint 18.2. Linux
kernel 4.15.0-lowlatency. The sage source directory is
/media/paul/str/source/sage (it's an external sd card). The log file is
around 12 MB(ending with the error message I copied) so I have created a
Google drive link to it:

https://drive.google.com/file/d/1uhm0WZ2eZ8N-Dj7RQ8sMSFjz_ourK1I_/view?usp=sharing.


Can anyone tell what is going wrong here? Is this a known bug? Thank you
for your help,
Paul

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Re: [sage-devel] Sage Compilation Error

[Dima Pasechnik]

This looks like a known bug, fixed in the latest beta I believe.

On Sun, 24 Feb 2019 19:42 Paul Clarke,  wrote:

> Hello,
> Sage failed during compilation of the gfortran component. It appears that
> the files were compiled successfully, but there was an error when copying
> them to their final destination.
>
> Here is the error message:
>
> [gfortran-7.2.0] Copying package files from temporary location
> /media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst to
> /media/paul/str/source/sage/local
> [gfortran-7.2.0] cp: cannot overwrite non-directory
> '/media/paul/str/source/sage/local/./lib64' with directory
> '/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst/media/paul/str/source/sage/local/./lib64'
> [gfortran-7.2.0]
> 
> [gfortran-7.2.0] Error copying files for gfortran-7.2.0.
> [gfortran-7.2.0]
> 
> [gfortran-7.2.0] Please email sage-devel (
> http://groups.google.com/group/sage-devel)
> [gfortran-7.2.0] explaining the problem and including the log file
> [gfortran-7.2.0]   /media/paul/str/source/sage/logs/pkgs/gfortran-7.2.0.log
> [gfortran-7.2.0] Describe your computer, operating system, etc.
> [gfortran-7.2.0]
> 
> Makefile:2124: recipe for target
> '/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0'
> failed
> make[3]: ***
> [/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0]
> Error 1
> make[3]: Leaving directory '/media/paul/str/source/sage/build/make'
> Makefile:1801: recipe for target 'all-start' failed
> make[2]: *** [all-start] Error 2
> make[2]: Leaving directory '/media/paul/str/source/sage/build/make'
>
> real35m24.461s
> user28m44.864s
> sys3m53.390s
> ***
>
> My computer is a chromebook pixel 2015 running linux mint 18.2. Linux
> kernel 4.15.0-lowlatency. The sage source directory is
> /media/paul/str/source/sage (it's an external sd card). The log file is
> around 12 MB(ending with the error message I copied) so I have created a
> Google drive link to it:
>
> https://drive.google.com/file/d/1uhm0WZ2eZ8N-Dj7RQ8sMSFjz_ourK1I_/view?usp=sharing.
>
>
> Can anyone tell what is going wrong here? Is this a known bug? Thank you
> for your help,
> Paul
>
> --
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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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Re: [sage-devel] Sage Compilation Error

[Paul Clarke]

 Don't think so, because it is copying to and from locations on 
/media/paul/str , which has 90 GB left on it. The root filesystem drive 
only has 1 GB left, though. 

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Re: [sage-devel] Sage Compilation Error

[Ike Stoddard]

Check disks for space?

On Sun, Feb 24, 2019 at 12:42 Paul Clarke  wrote:

> Hello,
> Sage failed during compilation of the gfortran component. It appears that
> the files were compiled successfully, but there was an error when copying
> them to their final destination.
>
> Here is the error message:
>
> [gfortran-7.2.0] Copying package files from temporary location
> /media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst to
> /media/paul/str/source/sage/local
> [gfortran-7.2.0] cp: cannot overwrite non-directory
> '/media/paul/str/source/sage/local/./lib64' with directory
> '/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst/media/paul/str/source/sage/local/./lib64'
> [gfortran-7.2.0]
> 
> [gfortran-7.2.0] Error copying files for gfortran-7.2.0.
> [gfortran-7.2.0]
> 
> [gfortran-7.2.0] Please email sage-devel (
> http://groups.google.com/group/sage-devel)
> [gfortran-7.2.0] explaining the problem and including the log file
> [gfortran-7.2.0]   /media/paul/str/source/sage/logs/pkgs/gfortran-7.2.0.log
> [gfortran-7.2.0] Describe your computer, operating system, etc.
> [gfortran-7.2.0]
> 
> Makefile:2124: recipe for target
> '/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0'
> failed
> make[3]: ***
> [/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0]
> Error 1
> make[3]: Leaving directory '/media/paul/str/source/sage/build/make'
> Makefile:1801: recipe for target 'all-start' failed
> make[2]: *** [all-start] Error 2
> make[2]: Leaving directory '/media/paul/str/source/sage/build/make'
>
> real35m24.461s
> user28m44.864s
> sys3m53.390s
> ***
>
> My computer is a chromebook pixel 2015 running linux mint 18.2. Linux
> kernel 4.15.0-lowlatency. The sage source directory is
> /media/paul/str/source/sage (it's an external sd card). The log file is
> around 12 MB(ending with the error message I copied) so I have created a
> Google drive link to it:
>
> https://drive.google.com/file/d/1uhm0WZ2eZ8N-Dj7RQ8sMSFjz_ourK1I_/view?usp=sharing.
>
>
> Can anyone tell what is going wrong here? Is this a known bug? Thank you
> for your help,
> Paul
>
> --
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> "sage-devel" group.
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> email to sage-devel+unsubscr...@googlegroups.com.
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>

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[sage-devel] Sage Compilation Error

[Paul Clarke]

Hello,
Sage failed during compilation of the gfortran component. It appears that 
the files were compiled successfully, but there was an error when copying 
them to their final destination. 

Here is the error message:

[gfortran-7.2.0] Copying package files from temporary location 
/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst to 
/media/paul/str/source/sage/local
[gfortran-7.2.0] cp: cannot overwrite non-directory 
'/media/paul/str/source/sage/local/./lib64' with directory 
'/media/paul/str/source/sage/local/var/tmp/sage/build/gfortran-7.2.0/inst/media/paul/str/source/sage/local/./lib64'
[gfortran-7.2.0] 

[gfortran-7.2.0] Error copying files for gfortran-7.2.0.
[gfortran-7.2.0] 

[gfortran-7.2.0] Please email sage-devel 
(http://groups.google.com/group/sage-devel)
[gfortran-7.2.0] explaining the problem and including the log file
[gfortran-7.2.0]   /media/paul/str/source/sage/logs/pkgs/gfortran-7.2.0.log
[gfortran-7.2.0] Describe your computer, operating system, etc.
[gfortran-7.2.0] 

Makefile:2124: recipe for target 
'/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0' 
failed
make[3]: *** 
[/media/paul/str/source/sage/local/var/lib/sage/installed/gfortran-7.2.0] 
Error 1
make[3]: Leaving directory '/media/paul/str/source/sage/build/make'
Makefile:1801: recipe for target 'all-start' failed
make[2]: *** [all-start] Error 2
make[2]: Leaving directory '/media/paul/str/source/sage/build/make'

real35m24.461s
user28m44.864s
sys3m53.390s
***

My computer is a chromebook pixel 2015 running linux mint 18.2. Linux 
kernel 4.15.0-lowlatency. The sage source directory is 
/media/paul/str/source/sage (it's an external sd card). The log file is 
around 12 MB(ending with the error message I copied) so I have created a 
Google drive link to it:
https://drive.google.com/file/d/1uhm0WZ2eZ8N-Dj7RQ8sMSFjz_ourK1I_/view?usp=sharing.
 


Can anyone tell what is going wrong here? Is this a known bug? Thank you 
for your help,
Paul

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[sage-devel] sage compilation crash and stop the pc

[Henri Girard]

Hi,

I used to compiled sage till version 7.0, but now it crashes and halt pc 
at about the compilation of doc (but I think with the last 8.2 beta 3 it 
was before because sage doesn't run). I have an AMD 8core and 16 Go RAM 
ssd 250 Go) ubuntu 17.10 (and 18.04). I guess I haven't enaugh RAM now ?


Would it be possible to have a binary somewhere so that it could be tested ?

Regards

Henri


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Re: [sage-devel] Sage compilation failure on CentOS 5.7

[Daniel Thau]

On Fri, Nov 11, 2011 at 07:15:27AM +1300, Francois Bissey wrote:
  On Wed, Nov 9, 2011 at 11:00 PM, Dan Drake dr...@kaist.edu wrote:
   On Wed, 09 Nov 2011 at 09:16PM -0500, Daniel Thau wrote:
Yeah, I considered that possibility.  The md5sum for both the
   
   pre-compiled
   
version I tried and the source both matched what they were expected
too.

$ md5sum sage-4.7.2.tar
b3073997e6c7ec00a269f84ff2e54973  sage-4.7.2.tar

Any other ideas?
   
   Okay, this will be harder then. The first weird thing to me is line 45
   of your paste:
   
   mv: cannot stat `/scratch/sage-4.7.2/devel/sage-main': No such file or
   directory
   
   That seems strange that the directory/symlink was not created. Maybe try
   re-installing the Sage library with
   
   ./sage -f spkg/standard/sage-4.7.2.spkg
   
   and see if that works.
   
   The only other thing I can think of right now is your version of gcc,
   which is pretty old. I don't know if that's the problem, though.
   
   
   Dan
   
   --
   ---  Dan Drake
   -  http://mathsci.kaist.ac.kr/~drake
   ---
  
  If it helps, I found that directory does in fact exist:
  
  ls /scratch/sage-4.7.2/devel/sage-main
  MANIFEST.in  README.txt  c_lib  export   module_list.py   pull  sage-push
  spkg-delauto  spkg-install
  PKG-INFO bundle  docinstall  module_list.pyc  sage  setup.py
  spkg-dist
  
  Running the command you recommended yielded the following:
  
  http://pastebin.com/2Qv8JTrG
  
  Still doesn't look good.  I'll see what I can do about getting a newer
  version of gcc on there.
 
 That's very strange.That's an error you would get if the file sage-sage 
 is corupted or edited slightly wrong. I got such an error in sage-on-gentoo
 when I removed a little bit too much stuff from sage-sage. 
 Would you have another sage install in your path by any chance?
 
 Francois
 
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 http://groups.google.com/group/sage-devel
 URL: http://www.sagemath.org

No, that was the only sage on the system.

I haven't been able to track down the problem with compiling quite yet,
but I did figure out the problem with running the pre-compiled sage:

The error I got was 

$ sage
python: can't open file 'show-all-if-ambiguous': [Errno 2] No such file
or directory

So naturally I started digging through Sage's source for
show-all-if-amiguous.  I tried commenting/removing it whenever I found
it, but none of it helped.  I accidentally searched in my $HOME rather
than in Sage's source while trying this and noticed my .bashrc had
'set show-all-if-ambiguous'.  Removing that fixed it!  This is particularly
weird, as I don't use bash - I use zsh.  As far as I know that file was
sitting idly on disk, and I don't understand why Sage would parse it or
if it did why that line would be problematic.

Now that I've figured it out I've got the pre-compiled version of sage
running fine.  This may also be related to the problem with compiling,
but I haven't had a chance to test it out yet.

Should I file a bug report?


signature.asc
Description: Digital signature

Re: [sage-devel] Sage compilation failure on CentOS 5.7

[Daniel Thau]

On Wed, Nov 9, 2011 at 11:00 PM, Dan Drake dr...@kaist.edu wrote:

 On Wed, 09 Nov 2011 at 09:16PM -0500, Daniel Thau wrote:
  Yeah, I considered that possibility.  The md5sum for both the
 pre-compiled
  version I tried and the source both matched what they were expected too.
 
  $ md5sum sage-4.7.2.tar
  b3073997e6c7ec00a269f84ff2e54973  sage-4.7.2.tar
 
  Any other ideas?

 Okay, this will be harder then. The first weird thing to me is line 45
 of your paste:

 mv: cannot stat `/scratch/sage-4.7.2/devel/sage-main': No such file or
 directory

 That seems strange that the directory/symlink was not created. Maybe try
 re-installing the Sage library with

 ./sage -f spkg/standard/sage-4.7.2.spkg

 and see if that works.

 The only other thing I can think of right now is your version of gcc,
 which is pretty old. I don't know if that's the problem, though.


 Dan

 --
 ---  Dan Drake
 -  http://mathsci.kaist.ac.kr/~drake
 ---


If it helps, I found that directory does in fact exist:

ls /scratch/sage-4.7.2/devel/sage-main
MANIFEST.in  README.txt  c_lib  export   module_list.py   pull  sage-push
spkg-delauto  spkg-install
PKG-INFO bundle  docinstall  module_list.pyc  sage  setup.py
spkg-dist

Running the command you recommended yielded the following:

http://pastebin.com/2Qv8JTrG

Still doesn't look good.  I'll see what I can do about getting a newer
version of gcc on there.

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Re: [sage-devel] Sage compilation failure on CentOS 5.7

[Francois Bissey]

 On Wed, Nov 9, 2011 at 11:00 PM, Dan Drake dr...@kaist.edu wrote:
  On Wed, 09 Nov 2011 at 09:16PM -0500, Daniel Thau wrote:
   Yeah, I considered that possibility.  The md5sum for both the
  
  pre-compiled
  
   version I tried and the source both matched what they were expected
   too.
   
   $ md5sum sage-4.7.2.tar
   b3073997e6c7ec00a269f84ff2e54973  sage-4.7.2.tar
   
   Any other ideas?
  
  Okay, this will be harder then. The first weird thing to me is line 45
  of your paste:
  
  mv: cannot stat `/scratch/sage-4.7.2/devel/sage-main': No such file or
  directory
  
  That seems strange that the directory/symlink was not created. Maybe try
  re-installing the Sage library with
  
  ./sage -f spkg/standard/sage-4.7.2.spkg
  
  and see if that works.
  
  The only other thing I can think of right now is your version of gcc,
  which is pretty old. I don't know if that's the problem, though.
  
  
  Dan
  
  --
  ---  Dan Drake
  -  http://mathsci.kaist.ac.kr/~drake
  ---
 
 If it helps, I found that directory does in fact exist:
 
 ls /scratch/sage-4.7.2/devel/sage-main
 MANIFEST.in  README.txt  c_lib  export   module_list.py   pull  sage-push
 spkg-delauto  spkg-install
 PKG-INFO bundle  docinstall  module_list.pyc  sage  setup.py
 spkg-dist
 
 Running the command you recommended yielded the following:
 
 http://pastebin.com/2Qv8JTrG
 
 Still doesn't look good.  I'll see what I can do about getting a newer
 version of gcc on there.

That's very strange.That's an error you would get if the file sage-sage 
is corupted or edited slightly wrong. I got such an error in sage-on-gentoo
when I removed a little bit too much stuff from sage-sage. 
Would you have another sage install in your path by any chance?

Francois

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[sage-devel] Sage compilation failure on CentOS 5.7

[Daniel Thau]

Hi,

I would like to be able to run Sage on a Centos 5.7 machine.

Simply downloading, untaring and running Sage 4.7.2 for RHEL 5.6
results in the following:

./sage
The Sage installation tree may have moved
(from /home/buildbot/build/sage/
rosemary-1/rosemary_binary/build/sage-4.7.2
to
/scratch/sage-4.7.2-linux-64bit-red_hat_enterprise_linux_server_release_5.6_tikanga-x86_64-Linux).
Changing various hardcoded paths...
(Please wait at most a few minutes.)
DO NOT INTERRUPT THIS.
Done resetting paths.
python: can't open file 'show-all-if-ambiguous': [Errno 2] No such
file or directory

That's alright; I'd rather build it from source to get whatever
benefits can result from that.  However, I am having trouble with that
as well.  Simply downloading the 4.7.2 source, untaring, and running
make results in errors.  The last hundred lines or so of the
install.log can be found here:

http://pastebin.com/RAXCRwBB

The problem doesn't seem to be about missing dependencies, or anything
else I could figure out on my own.

If more of the log - or any other  information - is necessary to help
debug this, let me know.

I decided to email sage-devel rather than sage-support due to the fact
that the install.log specifically instructed me to do so; if this
should go to sage-support let me know and I will make the request for
assistance there.

Thanks,
Daniel

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Re: [sage-devel] Sage compilation failure on CentOS 5.7

[Dan Drake]

On Wed, 09 Nov 2011 at 05:27PM -0500, Daniel Thau wrote:

 That's alright; I'd rather build it from source to get whatever
 benefits can result from that.  However, I am having trouble with that
 as well.  Simply downloading the 4.7.2 source, untaring, and running
 make results in errors.  The last hundred lines or so of the
 install.log can be found here:
 
 http://pastebin.com/RAXCRwBB
 
 The problem doesn't seem to be about missing dependencies, or anything
 else I could figure out on my own.

My guess is that your download is corrupted. is the md5sum
b3073997e6c7ec00a269f84ff2e54973 ? 

Dan

--
---  Dan Drake
-  http://mathsci.kaist.ac.kr/~drake
---


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Re: [sage-devel] Sage compilation failure on CentOS 5.7

[Daniel Thau]

On Wed, Nov 9, 2011 at 8:38 PM, Dan Drake dr...@kaist.edu wrote:

 On Wed, 09 Nov 2011 at 05:27PM -0500, Daniel Thau wrote:

  That's alright; I'd rather build it from source to get whatever
  benefits can result from that.  However, I am having trouble with that
  as well.  Simply downloading the 4.7.2 source, untaring, and running
  make results in errors.  The last hundred lines or so of the
  install.log can be found here:
 
  http://pastebin.com/RAXCRwBB
 
  The problem doesn't seem to be about missing dependencies, or anything
  else I could figure out on my own.

 My guess is that your download is corrupted. is the md5sum
 b3073997e6c7ec00a269f84ff2e54973 ?

 Dan

 --
 ---  Dan Drake
 -  http://mathsci.kaist.ac.kr/~drake
 ---


Yeah, I considered that possibility.  The md5sum for both the pre-compiled
version I tried and the source both matched what they were expected too.

$ md5sum sage-4.7.2.tar
b3073997e6c7ec00a269f84ff2e54973  sage-4.7.2.tar

Any other ideas?

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Re: [sage-devel] Sage compilation failure on CentOS 5.7

[Dan Drake]

On Wed, 09 Nov 2011 at 09:16PM -0500, Daniel Thau wrote:
 Yeah, I considered that possibility.  The md5sum for both the pre-compiled
 version I tried and the source both matched what they were expected too.
 
 $ md5sum sage-4.7.2.tar
 b3073997e6c7ec00a269f84ff2e54973  sage-4.7.2.tar
 
 Any other ideas?

Okay, this will be harder then. The first weird thing to me is line 45
of your paste: 

mv: cannot stat `/scratch/sage-4.7.2/devel/sage-main': No such file or
directory

That seems strange that the directory/symlink was not created. Maybe try
re-installing the Sage library with

./sage -f spkg/standard/sage-4.7.2.spkg

and see if that works.

The only other thing I can think of right now is your version of gcc,
which is pretty old. I don't know if that's the problem, though.


Dan

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