Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-16 Thread kcrisman


>
> > This has also been reported on devel [1,2] and might affect more Mac 
> users when upgrading to 8.9. Perhaps a copy of sage-dist-helpers could be 
> added back to src/bin for some deprecation period? 
>
> A symlink could do it. 
>

Very nice sleuthing all around.  I do recommend something be done for that 
as a stopgap for an 8.9rc - presumably it should also be tested out.  But 
for people who do not regularly upgrade to betas, but do build from source, 
this would be quite helpful. 

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-16 Thread E. Madison Bray
On Thu, Aug 15, 2019 at 6:58 PM Markus Wageringel
 wrote:
>
> This also happened to me a few weeks ago. The underlying problem seems to be 
> that the uninstall script fails because it tries to call sage-dist-helpers, 
> but cannot find it. This file has recently been moved from src/bin to 
> build/bin, which the uninstall script cannot know about. Once upgraded to Gap 
> 4.10.2.p0, it points to the new location of sage-dist-helpers, so this 
> particular problem should not happen again.

Good catch!

> This has also been reported on devel [1,2] and might affect more Mac users 
> when upgrading to 8.9. Perhaps a copy of sage-dist-helpers could be added 
> back to src/bin for some deprecation period?

A symlink could do it.

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-15 Thread John H Palmieri
Yes, that fits. Now that I know to look, I see buried in my gap install log 

Uninstalling existing 'gap'
Running pre-uninstall script for 'gap'
/Users/jpalmier/Desktop/Sage/git/sage/local/var/lib/sage/scripts/gap/spkg-prerm:
 
line 13: /Users/jpalmier/Desktop/Sage/git/sage/src/bin/sage-dist-helpers: 
No such file or directory
Error: failed to source sage-dist-helpers
Is /Users/jpalmier/Desktop/Sage/git/sage the correct SAGE_ROOT?
Error: The pre-uninstall script for 'gap' failed; the package will not be 
uninstalled, and some manual intervention may be needed to repair the 
package's state before uninstallation can proceed.  Check further up in 
this log for more details, or the pre-uninstall script itself at 
/Users/jpalmier/Desktop/Sage/git/sage/local/var/lib/sage/scripts/gap/spkg-prerm.



On Thursday, August 15, 2019 at 10:58:22 AM UTC-7, Markus Wageringel wrote:
>
> This also happened to me a few weeks ago. The underlying problem seems to 
> be that the uninstall script fails because it tries to call 
> sage-dist-helpers, but cannot find it. This file has recently been moved 
> from src/bin to build/bin, which the uninstall script cannot know about. 
> Once upgraded to Gap 4.10.2.p0, it points to the new location of 
> sage-dist-helpers, so this particular problem should not happen again.
>
> This has also been reported on devel [1,2] and might affect more Mac users 
> when upgrading to 8.9. Perhaps a copy of sage-dist-helpers could be added 
> back to src/bin for some deprecation period?
>
> [1] https://groups.google.com/forum/#!topic/sage-devel/cdw793St6cE
> [2] https://groups.google.com/forum/#!topic/sage-devel/h-hXvO2fxgc
>
>

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-15 Thread Markus Wageringel
This also happened to me a few weeks ago. The underlying problem seems to 
be that the uninstall script fails because it tries to call 
sage-dist-helpers, but cannot find it. This file has recently been moved 
from src/bin to build/bin, which the uninstall script cannot know about. 
Once upgraded to Gap 4.10.2.p0, it points to the new location of 
sage-dist-helpers, so this particular problem should not happen again.

This has also been reported on devel [1,2] and might affect more Mac users 
when upgrading to 8.9. Perhaps a copy of sage-dist-helpers could be added 
back to src/bin for some deprecation period?

[1] https://groups.google.com/forum/#!topic/sage-devel/cdw793St6cE
[2] https://groups.google.com/forum/#!topic/sage-devel/h-hXvO2fxgc

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-15 Thread E. Madison Bray
On Thu, Aug 15, 2019 at 2:22 PM kcrisman  wrote:
>
>
>> That's expected.  The package build directory is under SAGE_LOCAL
>> ($SAGE_LOCAL/var/tmp/sage/build/gap-4.10.0.p0) but the file's
>> destination path ($SAGE_LOCAL) is appended to this.  This is how it's
>> supposed to work (DESTDIR installation).
>>
>> It's probably too late to diagnose now (though it would be good if you
>> could give steps to reproduce).
>
>
> Yeah, unfortunately my main goal was getting a working Sage install, so the 
> evidence has been eliminated, so to speak.
>
>>
>>  But the question is what type of file
>> was
>>
>> /Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src
>>
>> that it refuses to overwrite because it was supposedly a directory?
>
>
>
> I can tell you a rough answer to that, after my most recent upgrade the name 
> of the directory seems to have changed slightly though:
>
> $ ls -l 
> ~/Downloads/sage/local/share/gap/bin/x86_64-apple-darwin15.6.0-default64-kv3/
>
> total 32
>
> lrwxr-xr-x  1 karl.crisman  78570554  18 Aug 14 14:39 config.h -> 
> ../../gen/config.h
>
> lrwxr-xr-x  1 karl.crisman  78570554   9 Aug 14 14:39 gac -> ../../gac
>
> lrwxr-xr-x  1 karl.crisman  78570554   9 Aug 14 14:39 gap -> ../../gap
>
> lrwxr-xr-x  1 karl.crisman  78570554   9 Aug 14 14:40 src -> ../../src
>
>
>>
>>
>> The GAP package installs a *symlink* at the path
>> $SAGE_LOCAL/share/gap/bin//src
>>
>
> So yes, that is what seems to be happening.
>
>>
>> When you upgrade GAP, first of all, it should be *uninstalling* the
>> previous gap package, so this link should just be removed.  The
>> question is was it a symlink for you in the first place?
>
>
> Apparently.

There was a bug fixed just a few months ago related to this:
https://trac.sagemath.org/ticket/27589

Symbolic links were not being removed properly.  They should be now,
though.  It's possible just from an older install something was left
behind.  Who knows...

>>  Or an actual
>> directory?  When you run `make clean-gap` does it get removed?
>>
>
> Is that something I can do from within Sage?  I didn't know that was a make 
> target for us.   My assumption is that the symlink was not removed or it 
> wouldn't have complained.

My mistake, that should be `make gap-clean`.  But yes, you can do that
from the base of SAGE_ROOT.  This also happens when you force
re-isinstall a package as with `./sage -f gap`.

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-15 Thread kcrisman


> That's expected.  The package build directory is under SAGE_LOCAL 
> ($SAGE_LOCAL/var/tmp/sage/build/gap-4.10.0.p0) but the file's 
> destination path ($SAGE_LOCAL) is appended to this.  This is how it's 
> supposed to work (DESTDIR installation). 
>
> It's probably too late to diagnose now (though it would be good if you 
> could give steps to reproduce). 


Yeah, unfortunately my main goal was getting a working Sage install, so the 
evidence has been eliminated, so to speak.
 

>  But the question is what type of file 
> was 
>
> /Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src
>  
>
>
> that it refuses to overwrite because it was supposedly a directory? 
>


I can tell you a rough answer to that, after my most recent upgrade the 
name of the directory seems to have changed slightly though:

$ ls -l 
~/Downloads/sage/local/share/gap/bin/x86_64-apple-darwin15.6.0-default64-kv3/

total 32

lrwxr-xr-x  1 karl.crisman  78570554  18 Aug 14 14:39 config.h -> 
../../gen/config.h

lrwxr-xr-x  1 karl.crisman  78570554   9 Aug 14 14:39 gac -> ../../gac

lrwxr-xr-x  1 karl.crisman  78570554   9 Aug 14 14:39 gap -> ../../gap

lrwxr-xr-x  1 karl.crisman  78570554   9 Aug 14 14:40 src -> ../../src
 

>
> The GAP package installs a *symlink* at the path 
> $SAGE_LOCAL/share/gap/bin//src 
>
>
So yes, that is what seems to be happening.
 

> When you upgrade GAP, first of all, it should be *uninstalling* the 
> previous gap package, so this link should just be removed.  The 
> question is was it a symlink for you in the first place?


Apparently.
 

>  Or an actual 
> directory?  When you run `make clean-gap` does it get removed? 
>
>
Is that something I can do from within Sage?  I didn't know that was a make 
target for us.   My assumption is that the symlink was not removed or it 
wouldn't have complained.

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-15 Thread E. Madison Bray
On Thu, Mar 7, 2019 at 5:50 PM kcrisman  wrote:
>
> upgrading from some early 8.6 beta, I get something weird with file 
> permissions on gap.  Everything seems to go well, but:
>
>
>
> pkg/laguna-3.9.0 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/polenta-1.3.8 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/polycyclic-2.14 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/resclasses-4.7.1 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/sophus-1.24 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/tomlib-1.2.7 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> ../gap -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/bin/gap
>
>
> real 2m48.230s
>
> user 1m30.082s
>
> sys 0m59.461s
>
> Copying package files from temporary location 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst to 
> /Users/.../sage/local
>
> cp: cannot overwrite directory 
> /Users/.../sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src 
> with non-directory 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src
>
> cp: /Users/.../sage/local/./share/gap/pkg/ctbllib/tst/docxpl.tst: Permission 
> denied
>
> 
>
> Error copying files for gap-4.10.0.p0.
>
> 
>
>
> I have a feeling that there is a typo of some kind in the commit
>
>
> https://github.com/sagemath/sage/commit/ca94bd97d73ee544c273fbb28cb774b3af12ecb6#diff-a9a04fa360dca60daa488241916fdb9c

I don't think so but...

> though I can't say immediately where, because the full line is
>
>
> non-directory 
> /Users/karl.crisman/Downloads/sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src
>
>
> and indeed I don't see why there should be a file that has the entire path to 
> sage/local TWICE; probably should use a temp file if for some reason that was 
> the desired behavior? I did not do anything unusual in this setup.

That's expected.  The package build directory is under SAGE_LOCAL
($SAGE_LOCAL/var/tmp/sage/build/gap-4.10.0.p0) but the file's
destination path ($SAGE_LOCAL) is appended to this.  This is how it's
supposed to work (DESTDIR installation).

It's probably too late to diagnose now (though it would be good if you
could give steps to reproduce).  But the question is what type of file
was

/Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src

that it refuses to overwrite because it was supposedly a directory?

The GAP package installs a *symlink* at the path
$SAGE_LOCAL/share/gap/bin//src

When you upgrade GAP, first of all, it should be *uninstalling* the
previous gap package, so this link should just be removed.  The
question is was it a symlink for you in the first place?  Or an actual
directory?  When you run `make clean-gap` does it get removed?

I think normally there hasn't been a problem with this, at least not
with consistent incremental updates, or else it would show up on the
patchbot.

In other words, I don't think you'll see this every time your gap
package updates.  But if you do that would be worth knowing about and
investigating.

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-14 Thread Dima Pasechnik
this is a MacOS only bug. Someone running it should work on fix...


On Wed, 14 Aug 2019 20:35 kcrisman,  wrote:

>
>
> On Friday, March 8, 2019 at 8:18:02 AM UTC-5, Dima Pasechnik wrote:
>>
>> On Fri, Mar 8, 2019 at 12:40 PM kcrisman  wrote:
>> >
>> >
>> >
>> > On Friday, March 8, 2019 at 3:24:45 AM UTC-5, Dima Pasechnik wrote:
>> >>
>> >> https://trac.sagemath.org/ticket/27388 fixed the permissions, but
>> >> because it's an upgrade from the state where there was a read-only
>> >> file, it breaks (on OSX only)
>> >
>> >
>> > Would that mean that, in general, upgrades from beta4 (which seems to
>> be the last version without this problem, according to one of the tickets)
>> via git pull and make will break indefinitely?  Should we have a blanket
>> recommendation to rebuild from scratch?
>>
>> this is too blanket :-)
>> e.g. in this particular case it suffices to manually remove
>> SAGE_LOCAL/share/gap
>> and rebuild gap spkg
>> (and then run make, naturally...)
>>
>
> Weirdly, I had to do this again even after the update mentioned here
> (apparently going from 8.7.beta6 to 8.9.beta6).   Is this likely to happen
> every time we upgrade GAP?
>
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> 
> .
>

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-08-14 Thread kcrisman


On Friday, March 8, 2019 at 8:18:02 AM UTC-5, Dima Pasechnik wrote:
>
> On Fri, Mar 8, 2019 at 12:40 PM kcrisman > 
> wrote: 
> > 
> > 
> > 
> > On Friday, March 8, 2019 at 3:24:45 AM UTC-5, Dima Pasechnik wrote: 
> >> 
> >> https://trac.sagemath.org/ticket/27388 fixed the permissions, but 
> >> because it's an upgrade from the state where there was a read-only 
> >> file, it breaks (on OSX only) 
> > 
> > 
> > Would that mean that, in general, upgrades from beta4 (which seems to be 
> the last version without this problem, according to one of the tickets) via 
> git pull and make will break indefinitely?  Should we have a blanket 
> recommendation to rebuild from scratch? 
>
> this is too blanket :-) 
> e.g. in this particular case it suffices to manually remove 
> SAGE_LOCAL/share/gap 
> and rebuild gap spkg 
> (and then run make, naturally...) 
>

Weirdly, I had to do this again even after the update mentioned here 
(apparently going from 8.7.beta6 to 8.9.beta6).   Is this likely to happen 
every time we upgrade GAP?

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-03-08 Thread kcrisman


> this is too blanket :-) 
> e.g. in this particular case it suffices to manually remove 
> SAGE_LOCAL/share/gap 
> and rebuild gap spkg 
> (and then run make, naturally...) 
>
>
Great, thanks!  Apparently that sufficed.
 

> Certainly there is never a guarantee that a "git pull"+"make" would 
> just work, as 
> the current state could be beyond repair... 
>
>
Yes, of course!  In this case I had a working Sage install at beta1 or 
beta2, though.

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-03-08 Thread Dima Pasechnik
On Fri, Mar 8, 2019 at 12:40 PM kcrisman  wrote:
>
>
>
> On Friday, March 8, 2019 at 3:24:45 AM UTC-5, Dima Pasechnik wrote:
>>
>> https://trac.sagemath.org/ticket/27388 fixed the permissions, but
>> because it's an upgrade from the state where there was a read-only
>> file, it breaks (on OSX only)
>
>
> Would that mean that, in general, upgrades from beta4 (which seems to be the 
> last version without this problem, according to one of the tickets) via git 
> pull and make will break indefinitely?  Should we have a blanket 
> recommendation to rebuild from scratch?

this is too blanket :-)
e.g. in this particular case it suffices to manually remove SAGE_LOCAL/share/gap
and rebuild gap spkg
(and then run make, naturally...)

Certainly there is never a guarantee that a "git pull"+"make" would
just work, as
the current state could be beyond repair...

> Thanks for any advice here - luckily from testing the app version I have some 
> still working Sage installs, but I like having my devel version separately 
> working.
>
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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-03-08 Thread kcrisman


On Friday, March 8, 2019 at 3:24:45 AM UTC-5, Dima Pasechnik wrote:
>
> https://trac.sagemath.org/ticket/27388 fixed the permissions, but 
> because it's an upgrade from the state where there was a read-only 
> file, it breaks (on OSX only) 
>

Would that mean that, in general, upgrades from beta4 (which seems to be 
the last version without this problem, according to one of the tickets) via 
git pull and make will break indefinitely?  Should we have a blanket 
recommendation to rebuild from scratch?  Thanks for any advice here - 
luckily from testing the app version I have some still working Sage 
installs, but I like having my devel version separately working.

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Re: [sage-release] Re: Sage 8.7.beta6 released

2019-03-08 Thread Dima Pasechnik
https://trac.sagemath.org/ticket/27388 fixed the permissions, but
because it's an upgrade from the state where there was a read-only
file, it breaks (on OSX only)

On Thu, Mar 7, 2019 at 4:50 PM kcrisman  wrote:
>
> upgrading from some early 8.6 beta, I get something weird with file 
> permissions on gap.  Everything seems to go well, but:
>
>
>
> pkg/laguna-3.9.0 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/polenta-1.3.8 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/polycyclic-2.14 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/resclasses-4.7.1 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/sophus-1.24 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> pkg/tomlib-1.2.7 -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/share/gap/pkg
>
> ../gap -> 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/bin/gap
>
>
> real 2m48.230s
>
> user 1m30.082s
>
> sys 0m59.461s
>
> Copying package files from temporary location 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst to 
> /Users/.../sage/local
>
> cp: cannot overwrite directory 
> /Users/.../sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src 
> with non-directory 
> /Users/.../sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/.../sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src
>
> cp: /Users/.../sage/local/./share/gap/pkg/ctbllib/tst/docxpl.tst: Permission 
> denied
>
> 
>
> Error copying files for gap-4.10.0.p0.
>
> 
>
>
> I have a feeling that there is a typo of some kind in the commit
>
>
> https://github.com/sagemath/sage/commit/ca94bd97d73ee544c273fbb28cb774b3af12ecb6#diff-a9a04fa360dca60daa488241916fdb9c
>
>
> though I can't say immediately where, because the full line is
>
>
> non-directory 
> /Users/karl.crisman/Downloads/sage/local/var/tmp/sage/build/gap-4.10.0.p0/inst/Users/karl.crisman/Downloads/sage/local/./share/gap/bin/x86_64-apple-darwin15.6.0-default64/src
>
>
> and indeed I don't see why there should be a file that has the entire path to 
> sage/local TWICE; probably should use a temp file if for some reason that was 
> the desired behavior? I did not do anything unusual in this setup.
>
>
> Thanks!  Everything else seems to be progressing normally.
>
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