Re: [sage-support] Condition of type: STORAGE-EXHAUSTED

[TAU]

On Fri, 20 Dec 2019, Jori Mantysalo wrote:

> On Fri, 20 Dec 2019, Mattia Villani wrote:
>
>> Here is my script:
>
> In my test the code seems to really eat much memory, so maybe it's not about 
> changing allocation between heap and stack. Maybe you just run out of memory.

I left the code to run to a computer with 64 GB RAM when leaving on 
vacation. However:

   File 
"/home/jm58660/sage/local/lib/python3.7/site-packages/sage/interfaces/maxima_lib.py",
 
line 986, in sr_limit
 return max_to_sr(maxima_eval(([max_limit], L)))
   File "sage/libs/ecl.pyx", line 805, in sage.libs.ecl.EclObject.__call__ 
(build/cythonized/sage/libs/ecl.c:7794)
   File "sage/libs/ecl.pyx", line 377, in sage.libs.ecl.ecl_safe_apply 
(build/cythonized/sage/libs/ecl.c:5456)
RuntimeError: ECL says: Maxima asks: Is 
(_SAGE_VAR_r^5-20*_SAGE_VAR_r^4+36*_SAGE_VAR_r^3+20*_SAGE_VAR_r^2+720)

*((_SAGE_VAR_r^15+72*_SAGE_VAR_r^13+20*_SAGE_VAR_r^12+1296*_SAGE_VAR_r^11
  +1440*_SAGE_VAR_r^10+25920*_SAGE_VAR_r^8)
  *%e^(40/_SAGE_VAR_r^3)
  +((-4*_SAGE_VAR_r^15)-288*_SAGE_VAR_r^13-80*_SAGE_VAR_r^12
   -5184*_SAGE_VAR_r^11-5760*_SAGE_VAR_r^10
   -103680*_SAGE_VAR_r^8)
   *%e^(20/_SAGE_VAR_r^3)+4*_SAGE_VAR_r^15+288*_SAGE_VAR_r^13
  +80*_SAGE_VAR_r^12+5184*_SAGE_VAR_r^11+5760*_SAGE_VAR_r^10
  +103680*_SAGE_VAR_r^8) positive, negative or zero?

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
   File "koe.sage.py", line 39, in 
 print(limit(limit(kr.expr().subs(m=_sage_const_10 ,L=_sage_const_1 
,A=_sage_const_6 ,alpha=_sage_const_2 ,beta=_sage_const_4 
),th=_sage_const_0 ),r=_sage_const_0 ))
   File 
"/home/jm58660/sage/local/lib/python3.7/site-packages/sage/calculus/calculus.py",
 
line 1368, in limit
 l = maxima.sr_limit(ex, v, a)
   File 
"/home/jm58660/sage/local/lib/python3.7/site-packages/sage/interfaces/maxima_lib.py",
 
line 990, in sr_limit
 self._missing_assumption(s)
   File 
"/home/jm58660/sage/local/lib/python3.7/site-packages/sage/interfaces/maxima_lib.py",
 
line 1035, in _missing_assumption
 raise ValueError(outstr)
ValueError: Computation failed since Maxima requested additional 
constraints; using the 'assume' command before evaluation *may* help 
(example of legal syntax is 'assume((r^5-20*r^4+36*r^3+20*r^2+720)
>0)', see `assume?` for more details)
Is (r^5-20*r^4+36*r^3+20*r^2+720)
 *((r^15+72*r^13+20*r^12+1296*r^11
  +1440*r^10+25920*r^8)
  *%e^(40/r^3)
  +((-4*r^15)-288*r^13-80*r^12
   -5184*r^11-5760*r^10
   -103680*r^8)
   *%e^(20/r^3)+4*r^15+288*r^13
  +80*r^12+5184*r^11+5760*r^10
  +103680*r^8) positive, negative or zero?


-- 
Jori Mäntysalo

Tampereen yliopisto - Ihminen ratkaisee

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[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Eric Martin]

I did not have ~/.sage. Removed org.sagemath.Sage.plist, but no difference 
for me.

On Monday, January 6, 2020 at 11:01:33 PM UTC+1, Stefano Brocco wrote:
>
> There is more to it: after doing all of the above, plus removing both 
> ~/.sage and org.sagemath.Sage.plist, the jupyter did start. Unfortunately I 
> don't know if the critical step in my case was the removal of ~/.sage or of 
> the plist file.
>
> On Monday, January 6, 2020 at 1:13:50 PM UTC-5, Eric Martin wrote:
>>
>> Same behaviour, with the same log, also after giving Sage Full Disk 
>> Access as suggested by Ralf Martin.
>>
>> On Monday, January 6, 2020 at 2:44:19 PM UTC+1, slelievre wrote:
>>>
>>>
>>> Mon 2020-01-06 10:04:35 UTC, Eric Martin:

 After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking

>>> the Sage icon immediately results in a window popping up with the 
 message:

>>> "Jupiter Server fails to start. For some reason the Jupiter server ailed 
 to start.

>>> [...]

>>>
>>> Try running the following commands in a terminal:
>>> 
>>> APP=/Applications/SageMath-9.0.app
>>> xattr -dr com.apple.quarantine $APP
>>>
>>> If it says you don't have the permissions for that,
>>> try the same with "sudo" as follows:
>>>
>>> APP=/Applications/SageMath-9.0.app
>>> sudo xattr -dr com.apple.quarantine $APP
>>>
>>>

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[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Stefano Brocco]

There is more to it: after doing all of the above, plus removing both 
~/.sage and org.sagemath.Sage.plist, the jupyter did start. Unfortunately I 
don't know if the critical step in my case was the removal of ~/.sage or of 
the plist file.

On Monday, January 6, 2020 at 1:13:50 PM UTC-5, Eric Martin wrote:
>
> Same behaviour, with the same log, also after giving Sage Full Disk Access 
> as suggested by Ralf Martin.
>
> On Monday, January 6, 2020 at 2:44:19 PM UTC+1, slelievre wrote:
>>
>>
>> Mon 2020-01-06 10:04:35 UTC, Eric Martin:
>>>
>>> After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking
>>>
>> the Sage icon immediately results in a window popping up with the message:
>>>
>> "Jupiter Server fails to start. For some reason the Jupiter server ailed 
>>> to start.
>>>
>> [...]
>>>
>>
>> Try running the following commands in a terminal:
>> 
>> APP=/Applications/SageMath-9.0.app
>> xattr -dr com.apple.quarantine $APP
>>
>> If it says you don't have the permissions for that,
>> try the same with "sudo" as follows:
>>
>> APP=/Applications/SageMath-9.0.app
>> sudo xattr -dr com.apple.quarantine $APP
>>
>>

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[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Stefano Brocco]

Same as Martin for me too...

On Monday, January 6, 2020 at 1:13:50 PM UTC-5, Eric Martin wrote:
>
> Same behaviour, with the same log, also after giving Sage Full Disk Access 
> as suggested by Ralf Martin.
>
>

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[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Murray Eisenberg]

Giving SageMath-9.0 full disk access works for me, too.

It seems like a rather blunt solution for getting around Catalina's 
increased security!

Is it full disk access that's really required? Or just the ability to 
launch a terminal process?

On Monday, January 6, 2020 at 5:04:35 AM UTC-5, Eric Martin wrote:
>
> After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking 
> the Sage icon immediately results in a window popping up with the message: 
> "Jupiter Server fails to start. For some reason the Jupiter server ailed to 
> start. Please check the log for clues, and have that information handy when 
> asking for help." The log shows:
>
> Rewriting paths for your new installation directory
> ===
>
> This might take a few minutes but only has to be done once.
>
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/build/make/Makefile-auto
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/config.status
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/2to3-3.7
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ESingular
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/NRswitchg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/QuadraticSieve
> patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/R
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Rscript
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Singular
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/TSingular
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/addedgeg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency_gmp
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces_gmp
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/amtog
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/annotate
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/biplabg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cas_help
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/catg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec_gmp
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cl
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/complg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/converseg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/copyg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/countg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cu2
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubex
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubhamg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/curve_keygen
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cygdb
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cysignals-CSI
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cython
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cythonize
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/deledgeg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/delptg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/directg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dreadnaut
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretodot
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretog
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install-3.7
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecl
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecl-config
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecm
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/f2py
> patching 
> 

[sage-support] Re: Lie algebra morphism, mutable matrices, basis not defined

[Travis Scrimshaw]

Hi Samuel,
   Both issues are tied to the matrix Lie algebra implementation:

sage: e1.monomial_coefficients()
NotImplementedError: the basis is not defined

For the immuability issue: probably what should be done is for the matrix 
Lie algebras, all elements should be made immutable. This is an easy enough 
fix with the class hierarchy I believe. I will create a ticket for this and 
cc you.

For the other issue: for Lie algebras that are defined from associative 
algebras, in general I cannot construct a basis for a generic Lie algebra 
in finite time (even to check if it is finite-dimensional, which is 
probably equivalent). So the safe thing to do was to just not do anything 
that required an explicit basis unless we knew it was the entire 
associative algebra. Now for the matrix Lie algebras (well, any Lie algebra 
constructed from a finite-dimensional associative algebra), we definitely 
can do better because we know it is finite-dimensional.

Now why it needs to get the elements expressed in the basis is because the 
morphism() does not require you to specify the image on the entire basis. 
It also might be too specialized right now with assuming the target is also 
a LieAlgebraWithStructureCoefficients.

Best,
Travis


On Saturday, January 4, 2020 at 1:16:24 AM UTC+10, slelievre wrote:
>
> Dear sage-support, 
>
> At Sage Days 106 we are trying to learn some of the 
> Lie algebra functionality in SageMath and have two 
> small questions regarding Lie algebra morphisms. 
>
> We define the Lie algebra sl_2(QQ) in two ways as follows: 
>
> sage: sl2 = lie_algebras.sl(QQ, 2, representation='matrix') 
> sage: sl2.inject_variables() 
> Defining e1, f1, h1 
> sage: sl2bis = LieAlgebra(QQ, {('e', 'h'): {'e': -2}, ('f', 'h'): 
> {'f': 2}, ('e', 'f'): {'h': 1}}, names='e, f, h') 
> sage: sl2bis.inject_variables() 
> Defining e, f, h 
>
> Trying to define a Lie algebra morphism between the two 
> fails with this error: 
>
> sage: sl2.morphism({e1: e, f1: f, h1: h}) 
> Traceback (most recent call last) 
> ... 
> TypeError: mutable matrices are unhashable 
>
> and I was wondering why the basis is not made 
> of immutable matrices. 
>
> Trying to define the morphism the other way around, 
> fails with this error: 
>
> sage: sl2bis.morphism({e: e1, f: f1, h: h1}) 
> Traceback (most recent call last) 
> ... 
> NotImplementedError: the basis is not defined 
>
> and I was wondering what is the problem here. 
>
> Kind regards, 
> Samuel Lelièvre 
>

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[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Eric Martin]

Same behaviour, with the same log, also after giving Sage Full Disk Access 
as suggested by Ralf Martin.

On Monday, January 6, 2020 at 2:44:19 PM UTC+1, slelievre wrote:
>
>
> Mon 2020-01-06 10:04:35 UTC, Eric Martin:
>>
>> After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking
>>
> the Sage icon immediately results in a window popping up with the message:
>>
> "Jupiter Server fails to start. For some reason the Jupiter server ailed 
>> to start.
>>
> [...]
>>
>
> Try running the following commands in a terminal:
> 
> APP=/Applications/SageMath-9.0.app
> xattr -dr com.apple.quarantine $APP
>
> If it says you don't have the permissions for that,
> try the same with "sudo" as follows:
>
> APP=/Applications/SageMath-9.0.app
> sudo xattr -dr com.apple.quarantine $APP
>
>

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[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Ralph Martin]

>
> I also gave Sage Full Disk Access (in Security -> Privacy preference 
> pane), as well as using xattr, as it seemed unable to access certain 
> directories.
>
 

> Sage now does start Jupyter.
>
 

>
>
On Monday, 6 January 2020 15:07:35 UTC, Murray Eisenberg wrote:
>
> I separately reported the same behavior -- the Jupyter server not starting 
> with SageMath-9.0 -- and so tried the suggestion of 
>
> APP=/Applications/SageMath-9.0.app 
>
> xattr -dr com.apple.quarantine $APP
>
>
> reportedthe latter both as shown and with "sudo". 
>
>
> This does *not* fix the problem!
>
> On Monday, January 6, 2020 at 5:04:35 AM UTC-5, Eric Martin wrote:
>>
>> After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking 
>> the Sage icon immediately results in a window popping up with the message: 
>> "Jupiter Server fails to start. For some reason the Jupiter server ailed to 
>> start. Please check the log for clues, and have that information handy when 
>> asking for help." The log shows:
>>
>> Rewriting paths for your new installation directory
>> ===
>>
>> This might take a few minutes but only has to be done once.
>>
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/build/make/Makefile-auto
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/config.status
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/2to3-3.7
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ESingular
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/NRswitchg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/QuadraticSieve
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/R
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Rscript
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Singular
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/TSingular
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/addedgeg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency_gmp
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces_gmp
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/amtog
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/annotate
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/biplabg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cas_help
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/catg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec_gmp
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cl
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/complg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/converseg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/copyg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/countg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cu2
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubex
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubhamg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/curve_keygen
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cygdb
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cysignals-CSI
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cython
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cythonize
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/deledgeg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/delptg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/directg
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dreadnaut
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretodot
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretog
>> patching 
>> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install
>> patching 
>> 

[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Murray Eisenberg]

I separately reported the same behavior -- the Jupyter server not starting 
with SageMath-9.0 -- and so tried the suggestion of 

APP=/Applications/SageMath-9.0.app 

xattr -dr com.apple.quarantine $APP


reportedthe latter both as shown and with "sudo". 


This does *not* fix the problem!

On Monday, January 6, 2020 at 5:04:35 AM UTC-5, Eric Martin wrote:
>
> After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking 
> the Sage icon immediately results in a window popping up with the message: 
> "Jupiter Server fails to start. For some reason the Jupiter server ailed to 
> start. Please check the log for clues, and have that information handy when 
> asking for help." The log shows:
>
> Rewriting paths for your new installation directory
> ===
>
> This might take a few minutes but only has to be done once.
>
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/build/make/Makefile-auto
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/config.status
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/2to3-3.7
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ESingular
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/NRswitchg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/QuadraticSieve
> patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/R
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Rscript
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Singular
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/TSingular
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/addedgeg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency_gmp
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces_gmp
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/amtog
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/annotate
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/biplabg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cas_help
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/catg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec_gmp
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cl
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/complg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/converseg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/copyg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/countg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cu2
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubex
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubhamg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/curve_keygen
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cygdb
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cysignals-CSI
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cython
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cythonize
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/deledgeg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/delptg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/directg
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dreadnaut
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretodot
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretog
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install-3.7
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecl
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecl-config
> patching 
> /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecm
> patching 
> 

[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[slelievre]

Mon 2020-01-06 10:04:35 UTC, Eric Martin:
>
> After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking
>
the Sage icon immediately results in a window popping up with the message:
>
"Jupiter Server fails to start. For some reason the Jupiter server ailed to 
> start.
>
[...]
>

Try running the following commands in a terminal:

APP=/Applications/SageMath-9.0.app
xattr -dr com.apple.quarantine $APP

If it says you don't have the permissions for that,
try the same with "sudo" as follows:

APP=/Applications/SageMath-9.0.app
sudo xattr -dr com.apple.quarantine $APP

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[sage-support] Re: Offline help with Sage 9.0 from jupyter notebook did not work

[Eric Gourgoulhon]

Just a data point: "*Help - > Sage Documentation" in the Jupyter notebook 
works with Sage 9.0 built from source in Ubuntu 18.04.*


*Eric. *

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Re: [sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Dima Pasechnik]

On Mon, 6 Jan 2020, 13:18 Ralph Martin,  wrote:

> I confirm that Jupyter does not start. My log shows the following output
>
> [I 18:14:07.652 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
> [I 18:14:07.842 NotebookApp] Serving notebooks from local directory:
> /Users/ralph/Documents/Sage Jupyter Notebooks
> [I 18:14:07.842 NotebookApp] The Jupyter Notebook is running at:
> [I 18:14:07.843 NotebookApp]
> http://localhost:/?token=1c3d72103aad6145315688067632cb508eed65dc7b3ff57a
> [I 18:14:07.843 NotebookApp] Use Control-C to stop this server and shut
> down all kernels (twice to skip confirmation).
> [C 18:14:07.847 NotebookApp]
>
> To access the notebook, open this file in a browser:
>
> file:///Users/ralph/Library/Jupyter/runtime/nbserver-11902-open.html
> Or copy and paste one of these URLs:
>
> http://localhost:/?token=1c3d72103aad6145315688067632cb508eed65dc7b3ff57a
>

does this URL work?

[I 18:14:24.013 NotebookApp] Creating new notebook in
> [I 18:14:24.692 NotebookApp] Kernel started:
> 35543d18-9b4d-44d6-9234-fde888a4951e
> [I 18:14:26.123 NotebookApp] Adapting to protocol v5.1 for kernel
> 35543d18-9b4d-44d6-9234-fde888a4951e
> [I 18:15:11.689 NotebookApp] Saving file at /Untitled.ipynb
> [I 18:15:48.066 NotebookApp] Starting buffering for
> 35543d18-9b4d-44d6-9234-fde888a4951e:08c6751af6b3477893d056fe2cc9c4c7
> [I 18:15:48.379 NotebookApp] Kernel shutdown:
> 35543d18-9b4d-44d6-9234-fde888a4951e
> shell-init: error retrieving current directory: getcwd: cannot access
> parent directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access
> parent directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access
> parent directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access
> parent directories: Operation not permitted
> shell-init: error retrieving current directory: getcwd: cannot access
> parent directories: Operation not permitted
>
> --
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> "sage-support" group.
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> 
> .
>

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[sage-support] Re: Jupiter Server fails to start on macOS Catalina

[Ralph Martin]

I confirm that Jupyter does not start. My log shows the following output

[I 18:14:07.652 NotebookApp] Using MathJax: nbextensions/mathjax/MathJax.js
[I 18:14:07.842 NotebookApp] Serving notebooks from local directory: 
/Users/ralph/Documents/Sage Jupyter Notebooks
[I 18:14:07.842 NotebookApp] The Jupyter Notebook is running at:
[I 18:14:07.843 NotebookApp] 
http://localhost:/?token=1c3d72103aad6145315688067632cb508eed65dc7b3ff57a
[I 18:14:07.843 NotebookApp] Use Control-C to stop this server and shut 
down all kernels (twice to skip confirmation).
[C 18:14:07.847 NotebookApp] 

To access the notebook, open this file in a browser:
file:///Users/ralph/Library/Jupyter/runtime/nbserver-11902-open.html
Or copy and paste one of these URLs:

http://localhost:/?token=1c3d72103aad6145315688067632cb508eed65dc7b3ff57a
[I 18:14:24.013 NotebookApp] Creating new notebook in 
[I 18:14:24.692 NotebookApp] Kernel started: 
35543d18-9b4d-44d6-9234-fde888a4951e
[I 18:14:26.123 NotebookApp] Adapting to protocol v5.1 for kernel 
35543d18-9b4d-44d6-9234-fde888a4951e
[I 18:15:11.689 NotebookApp] Saving file at /Untitled.ipynb
[I 18:15:48.066 NotebookApp] Starting buffering for 
35543d18-9b4d-44d6-9234-fde888a4951e:08c6751af6b3477893d056fe2cc9c4c7
[I 18:15:48.379 NotebookApp] Kernel shutdown: 
35543d18-9b4d-44d6-9234-fde888a4951e
shell-init: error retrieving current directory: getcwd: cannot access 
parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access 
parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access 
parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access 
parent directories: Operation not permitted
shell-init: error retrieving current directory: getcwd: cannot access 
parent directories: Operation not permitted

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Re: [sage-support] Sage not loading after conda install (Catalina)

[Isuru Fernando]

I'm not a Mac user, so not sure about what's needed.

Can you try the solution in
https://support.apple.com/en-gb/guide/mac-help/mh40616/mac or
https://community.wappler.io/t/solving-python-error-in-macos-catalina-when-using-docker/13497
?

Isuru



On Mon, Jan 6, 2020 at 3:51 PM Christian Bean 
wrote:

> After following the instructions from
> http://doc.sagemath.org/html/en/installation/conda.html, with python=3,
> opening sage then failed. My computer is macOS Catalina 10.15.2. I have
> attached the crash report.
>
> https://hastebin.com/oleluxotoq.pl
>
> --
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> 
> .
>

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[sage-support] Sage not loading after conda install (Catalina)

[Christian Bean]

After following the instructions from 
http://doc.sagemath.org/html/en/installation/conda.html, with python=3, 
opening sage then failed. My computer is macOS Catalina 10.15.2. I have 
attached the crash report. 

https://hastebin.com/oleluxotoq.pl

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[sage-support] Failed Sage 9.0 build on Catalina

[Christian Bean]

I attempted to install Sage 9.0 on my Mac (macOS Catalina 10.15.2). 
Unfortunately, the build failed. I attached some log files of the failed 
build. I have installed brew and command line tools. 

ccache-3.3.4.log: https://hastebin.com/agazivozeh.coffeescript

openssl-1.1.1b.log: https://hastebin.com/ibiwibepax.coffeescript

patch-2.7.5.log: https://hastebin.com/imeyihozub.bash

config.log: https://hastebin.com/wukayudaqa.makefile

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[sage-support] Jupiter Server fails to start on macOS Catalina

[Eric Martin]

After installing sage-9.0-OSX_10.15.2-x86_64.app.dmg, doubling clicking the 
Sage icon immediately results in a window popping up with the message: 
"Jupiter Server fails to start. For some reason the Jupiter server ailed to 
start. Please check the log for clues, and have that information handy when 
asking for help." The log shows:

Rewriting paths for your new installation directory
===

This might take a few minutes but only has to be done once.

patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/build/make/Makefile-auto
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/config.status
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/2to3-3.7
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ESingular
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/NRswitchg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/QuadraticSieve
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/R
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Rscript
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/Singular
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/TSingular
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/addedgeg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/adjacency_gmp
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/allfaces_gmp
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/amtog
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/annotate
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/biplabg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cas_help
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/catg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cddexec_gmp
patching /Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cl
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/complg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/converseg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/copyg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/countg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cu2
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubex
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cubhamg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/curve_keygen
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cygdb
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cysignals-CSI
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cython
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/cythonize
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/deledgeg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/delptg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/directg
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dreadnaut
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretodot
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/dretog
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/easy_install-3.7
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecl
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecl-config
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/ecm
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/f2py
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/f2py3
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/f2py3.7
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fai
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fflas-ffpack-config
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fourier
patching 
/Applications/SageMath-9.0.app/Contents/Resources/sage/local/bin/fourier_gmp
patching