doctests: Filter out linker warning messages #31204

mkoeppe · 2021-01-07T21:43:55Z

On OS X Big Sur + various homebrew packages, if I use

% ./configure --with-system-python3=no --enable-download-from-upstream-url

then Sage builds (if I also incorporate various other changes from #30651), but I get doctest failures of the form

File "src/sage/misc/sagedoc.py", line 646, in sage.misc.sagedoc.format
Failed example:
    cython('\n'.join(cython_code))
Expected nothing
Got:
    ld: warning: dylib (/usr/local/lib/libmpfr.dylib) was built for newer macOS version (11.0) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgmp.dylib) was built for newer macOS version (11.0) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgmpxx.dylib) was built for newer macOS version (11.0) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libgsl.dylib) was built for newer macOS version (11.0) than being linked (10.9)
    ld: warning: dylib (/usr/local/lib/libntl.dylib) was built for newer macOS version (11.0) than being linked (10.9)

We should filter out these warnings in doctesting.

CC: @jhpalmieri @dimpase @kiwifb

Component: doctest framework

Author: John Palmieri

Branch/Commit: 55cf2ee

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/31204

The text was updated successfully, but these errors were encountered:

jhpalmieri · 2021-01-08T00:04:02Z

comment:1

I've only seen this on OS X. The following has worked for me, although it hasn't been thoroughly tested:

diff --git a/src/sage/doctest/parsing.py b/src/sage/doctest/parsing.py
index 4e1a6b32e4..77f726a27b 100644
--- a/src/sage/doctest/parsing.py
+++ b/src/sage/doctest/parsing.py
@@ -40,6 +40,8 @@ optional_regex = re.compile(r'(arb216|arb218|py2|py3|long time|not implemented|n
 # which has not been patched, we need to ignore that message.
 # See :trac:`29317`.
 glpk_simplex_warning_regex = re.compile(r'(Long-step dual simplex will be used)')
+# :trac:`31204` -- suppress warning about ld and OS version for dylib files.
+ld_warning_regex = re.compile(r'ld: warning: dylib.*was built for newer macOS version .* than being linked.*')
 find_sage_prompt = re.compile(r"^(\s*)sage: ", re.M)
 find_sage_continuation = re.compile(r"^(\s*)\.\.\.\.:", re.M)
 find_python_continuation = re.compile(r"^(\s*)\.\.\.([^\.])", re.M)
@@ -1087,6 +1089,7 @@ class SageOutputChecker(doctest.OutputChecker):
         """
         got = self.human_readable_escape_sequences(got)
         got = glpk_simplex_warning_regex.sub('', got)
+        got = ld_warning_regex.sub('', got)
         if isinstance(want, MarkedOutput):
             if want.random:
                 return True

I can produce a branch easily enough.

mkoeppe · 2021-01-08T00:32:01Z

comment:2

Looks fine to me. I briefly looked to find instances of this on Linux in GH Actions logs, but did not find anything, it's likely that I have confused this with something else.

jhpalmieri · 2021-01-08T04:26:30Z

comment:3

This doesn't quite catch all of the warnings:

**********************************************************************
File "src/sage/tests/cmdline.py", line 301, in sage.tests.cmdline.test_executable
Failed example:
    err
Expected:
    'Compiling ...spyx...'
Got:
    'Compiling /Users/palmieri/.sage/temp/John-iMac-2017.local/34214/dir__zddcuog/sage_test_file.spyx...\nld: warning: dylib (/usr/local/lib/libgmp.dylib) was built for newer macOS version (11.0) than being linked (10.9)\nld: warning: dylib (/usr/local/lib/libmpfr.dylib) was built for newer macOS version (11.0) than being linked (10.9)\nld: warning: dylib (/usr/local/lib/libgmpxx.dylib) was built for newer macOS version (11.0) than being linked (10.9)\nld: warning: dylib (/usr/local/lib/libgsl.dylib) was built for newer macOS version (11.0) than being linked (10.9)\nld: warning: dylib (/usr/local/lib/libntl.dylib) was built for newer macOS version (11.0) than being linked (10.9)\n'
**********************************************************************
File "src/sage/tests/cmdline.py", line 308, in sage.tests.cmdline.test_executable
Failed example:
    err
Expected:
    'Compiling ...spyx...'
Got:
    'Compiling sage_test_file.spyx...\nld: warning: dylib (/usr/local/lib/libgmp.dylib) was built for newer macOS version (11.0) than being linked (10.9)\nld: warning: dylib (/usr/local/lib/libmpfr.dylib) was built for newer macOS version (11.0) than being linked (10.9)\nld: warning: dylib (/usr/local/lib/libgmpxx.dylib) was built for newer macOS version (11.0) than being linked (10.9)\nld: warning: dylib (/usr/local/lib/libgsl.dylib) was built for newer macOS version (11.0) than being linked (10.9)\nld: warning: dylib (/usr/local/lib/libntl.dylib) was built for newer macOS version (11.0) than being linked (10.9)\n'
**********************************************************************
1 item had failures:
   2 of 231 in sage.tests.cmdline.test_executable

I'm not sure why the "..." doesn't capture all of this. Maybe it matches the verbatim "..." in the doctest output, or maybe it doesn't capture multiline strings.

mkoeppe · 2021-01-08T19:32:31Z

comment:4

Could you push a branch please?

jhpalmieri · 2021-01-08T19:49:38Z

Branch: u/jhpalmieri/31204-ld-warnings

jhpalmieri · 2021-01-08T19:50:40Z

comment:6

Replying to @mkoeppe:

Could you push a branch please?

Sure.

New commits:

`bb6edf6`	`trac 31204: suppress ld warning messages about wrong OS X version`

jhpalmieri · 2021-01-08T19:50:40Z

Commit: bb6edf6

sagetrac-git · 2021-01-31T22:20:12Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`801c1a7`	`trac 31204: suppress ld warning messages about wrong OS X version`

sagetrac-git · 2021-01-31T22:20:12Z

Changed commit from bb6edf6 to 801c1a7

jhpalmieri · 2021-01-31T22:21:18Z

comment:8

I modified the filter a bit, starting it with "dylib..." instead of "ld: warning: dylib...", since I've seen a few cases without "ld: warning".

zlscherr · 2021-02-03T01:24:49Z

comment:9

I was doing some testing today and could, for example, eliminate these warnings by doing something like:

MACOSX_DEPLOYMENT_TARGET=11.0 ./sage -t --random-seed=0 src/sage/docs/instancedoc.pyx

I think the underlying problem lies in the python that sage is using. You can see this, for example, by running sage and trying

import sysconfig
sysconfig.get_config_var("MACOSX_DEPLOYMENT_TARGET")

the issue is that the homebrew libraries were built on a particular operating system with its own deployment target, which is newer than the python target of sage. This problem also manifests itself in #31227 where /usr/bin/python3 has the target set to 10.14.6 for some reason.

I wonder if you can try to fix this by making sage set MACOSX_DEPLOYMENT_TARGET environment variable when it's run. You can probably get away with just setting it to whatever version of the Mac operating system you are on.

jhpalmieri · 2021-02-03T02:36:16Z

comment:10

I like the idea but I'm not getting it to work:

% MACOSX_DEPLOYMENT_TARGET=11.2 ./sage
┌────────────────────────────────────────────────────────────────────┐
│ SageMath version 9.3.beta6, Release Date: 2021-01-17               │
│ Using Python 3.9.1. Type "help()" for help.                        │
└────────────────────────────────────────────────────────────────────┘
┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Warning: this is a prerelease version, and it may be unstable.     ┃
┗━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┛
sage: import sysconfig                                                                    
sage: sysconfig.get_config_var("MACOSX_DEPLOYMENT_TARGET")                                
'10.9'

Maybe part of the solution is #18272: we should not be artificially setting MACOSX_DEPLOYMENT_TARGET. That may only help when we are using Sage's own Python, but I think this problem also arises with /usr/bin/python3 or the homebrew Python 3.

zlscherr · 2021-02-03T02:46:25Z

comment:11

What happen's if you try

MACOSX_DEPLOYMENT_TARGET=11.0 ./sage -t src/sage/misc/sagedoc.py

That won't change sysconfig's deployment target, but it might stop the linking warnings.

(I just ran make distclean for some reason and won't be able to test until tomorrow)

zlscherr · 2021-02-03T18:29:26Z

comment:12

ok, that definitely didn't work. For some reason that seemed to work with /usr/bin/python3 but not with the sage built python which is built for target 10.9

kiwifb · 2021-02-03T19:40:52Z

comment:13

We should definitely stop arbitrarily defining MACOSX_DEPLOYMENT_TARGET, the main use for it is producing binaries that are backward compatible up to a point. We shouldn't have any business setting it to something else than the host building system value unless we make a binary build.

jhpalmieri · 2021-02-04T04:12:28Z

comment:14

I've posted a branch at #18272 to stop defining MACOSX_DEPLOYMENT_TARGET. I've only tested it on Big Sur, but so far it's pretty good. I am still hitting these "ld" warning messages when building with /usr/bin/python3 (but not with homebrew or with Sage's own Python), so we will still need this ticket. I'm testing whether

% MACOSX_DEPLOYMENT_TARGET=11.0 make ptestlong

works when Sage is built with /usr/bin/python3 on top of #18272.

jhpalmieri · 2021-02-04T04:18:18Z

comment:15

Marking as "needs info" because the suggestion from comment:9 may be the right approach, and it would be better than filtering out the warnings.

jhpalmieri · 2021-02-04T19:15:01Z

comment:16

I like gh-zlscherr's suggestion, but what is the right way to do it?

unconditionally (on OS X only, I mean) set MACOSX_DEPLOYMENT_TARGET before running doctests?
set it conditionally based on some test of Python? If so, what test?
don't set it at all, but print a message (either always or conditionally) suggesting that the user might set it?
something else?

Do we set it in src/bin/sage-runtests or somewhere else?

jhpalmieri · 2021-03-13T21:58:26Z

comment:18

Maybe we should filter out the warnings and on separate tickets deal with the underlying issue of setting MACOSX_DEPLOYMENT_TARGET. For example: I don't see the warnings at all on OS X 11.2 using homebrew's Python, but when Sage builds its own Python, I can't eliminate the warnings by setting MACOSX_DEPLOYMENT_TARGET during doctesting.

mkoeppe · 2021-03-13T22:16:48Z

comment:19

+1 for this strategy.

Let's get this ticket into Sage 9.3. https://github.com/mkoeppe/sage/actions/runs/649866485 tests this ticket together with #31492 - but there seems to be a scarcity of macOS runners on GH Actions at the moment

mkoeppe · 2021-03-13T22:17:45Z

Author: John Palmieri

mkoeppe · 2021-03-14T08:23:21Z

comment:21

This regexp does not seem to be working for me

sagetrac-git · 2021-03-14T18:43:47Z

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

`288579d`	`trac 31204: suppress ld warning messages about wrong OS X version`
`e067c72`	`trac 31204: fix regexp`

sagetrac-git · 2021-03-14T18:43:47Z

Changed commit from 801c1a7 to e067c72

jhpalmieri · 2021-03-14T18:44:02Z

comment:23

Try this one.

mkoeppe · 2021-03-14T18:52:16Z

comment:24

The example from comment:3 is still a problem

jhpalmieri · 2021-03-14T18:59:08Z

comment:25

Replying to @mkoeppe:

The example from comment:3 is still a problem

It is, and the only thing I can think is to change the doctest:

diff --git a/src/sage/tests/cmdline.py b/src/sage/tests/cmdline.py
index 086704317f..82f825321b 100644
--- a/src/sage/tests/cmdline.py
+++ b/src/sage/tests/cmdline.py
@@ -292,15 +292,16 @@ def test_executable(args, input="", timeout=100.0, pydebug_ignore_warnings=False
         sage: (out, err, ret) = test_executable(["sage", fullname], pydebug_ignore_warnings=True)
         sage: print(out)
         499500
-        sage: err
-        'Compiling ...spyx...'
+        sage: import re
+        sage: bool(re.match('Compiling.*spyx.*', err))
+        True
         sage: ret
         0
         sage: (out, err, ret) = test_executable(["sage", name], cwd=dir, pydebug_ignore_warnings=True)
         sage: print(out)
         499500
-        sage: err
-        'Compiling ...spyx...'
+        sage: bool(re.match('Compiling.*spyx.*', err))
+        True
         sage: ret
         0

What do you think about that?

mkoeppe · 2021-03-14T19:30:59Z

comment:26

Fine with me to change these doctests, could you push it to the ticket please?

sagetrac-git · 2021-03-14T19:45:45Z

Changed commit from e067c72 to 55cf2ee

sagetrac-git · 2021-03-14T19:45:45Z

Branch pushed to git repo; I updated commit sha1. New commits:

`55cf2ee`	`trac 31204: fix one doctest`

mkoeppe · 2021-03-14T23:28:28Z

comment:28

This works well.

mkoeppe · 2021-03-14T23:28:28Z

Reviewer: Matthias Koeppe

jhpalmieri · 2021-03-14T23:59:46Z

comment:29

Good, thanks!

vbraun · 2021-03-18T22:32:31Z

Changed branch from u/jhpalmieri/31204-ld-warnings to 55cf2ee

mkoeppe added this to the sage-9.3 milestone Jan 7, 2021

mkoeppe added c: doctest framework labels Jan 7, 2021

jhpalmieri added the s: needs review label Jan 8, 2021

jhpalmieri added s: needs info and removed s: needs review labels Feb 4, 2021

mkoeppe added p: critical / 2 and removed p: major / 3 labels Mar 13, 2021

mkoeppe removed the s: needs info label Mar 13, 2021

mkoeppe added the s: needs review label Mar 13, 2021

mkoeppe added s: needs work and removed s: needs review labels Mar 14, 2021

jhpalmieri added s: needs review and removed s: needs work labels Mar 14, 2021

mkoeppe added s: positive review and removed s: needs review labels Mar 14, 2021

vbraun removed the s: positive review label Mar 18, 2021

vbraun closed this as completed in 3a6e07d Mar 18, 2021

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doctests: Filter out linker warning messages #31204

doctests: Filter out linker warning messages #31204

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