I think I've narrowed it down a little bit more. Inside the chroot,
root can run sage with R without errors. Looking at a diff of the
straces, when root runs sage, it opens /usr/lib/locale/locale-archive
but it doesn't if it's run as the sage user:
Root -
brk(0) = 0xcaad000
brk(0xcace000) = 0xcace000
open("/usr/lib/locale/locale-archive", O_RDONLY) = 3
fstat(3, {st_mode=S_IFREG|0644, st_size=56406016, ...}) = 0
mmap(NULL, 56406016, PROT_READ, MAP_PRIVATE, 3, 0) = 0x2b40de7c6000
close(3) = 0
execve("/usr/kerberos/sbin/bash", ["bash", "/home/sage/sage", "-c",
"r.version()"], [/* 23 vars */]) = -1 ENOENT (No such file or directory)
execve("/usr/kerberos/bin/bash", ["bash", "/home/sage/sage", "-c",
"r.version()"], [/* 23 vars */]) = -1 ENOENT (No such file or directory)
execve("/usr/local/sbin/bash", ["bash", "/home/sage/sage", "-c",
"r.version()"], [/* 23 vars */]) = -1 ENOENT (No such file or directory)
execve("/usr/local/bin/bash", ["bash", "/home/sage/sage", "-c",
"r.version()"], [/* 23 vars */]) = -1 ENOENT (No such file or directory)
execve("/sbin/bash", ["bash", "/home/sage/sage", "-c", "r.version()"],
[/* 23 vars */]) = -1 ENOENT (No such file or directory)
execve("/bin/bash", ["bash", "/home/sage/sage", "-c", "r.version()"],
[/* 23 vars */]) = 0
brk(0) = 0xbf4d000
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0)
= 0x2b47bb169000
Sage -
brk(0) = 0x5955000
brk(0x5976000) = 0x5976000
execve("/usr/local/bin/bash", ["bash", "./sage", "-t",
"devel/sage/sage/interfaces/expec"...], [/* 16 vars */]) = -1 ENOENT (No
such file or directory)
execve("/bin/bash", ["bash", "./sage", "-t",
"devel/sage/sage/interfaces/expec"...], [/* 16 vars */]) = 0
brk(0) = 0x110d000
mmap(NULL, 4096, PROT_READ|PROT_WRITE, MAP_PRIVATE|MAP_ANONYMOUS, -1, 0)
= 0x2b38ae1e7000
Any ideas?
Thanks,
Kay
Kay wrote:
> Hi all,
>
> First, thanks for all your hard work in these wonderful project! The
> folks at my institution are just in love with it.
>
> I'm trying to set up a notebook server in a chroot for them. The
> chroot, notebook, etc. seem to be working fine except for R. These
> are the tests that fail:
>
> sage -t "devel/sage/sage/interfaces/expect.py"
> sage -t "devel/sage/sage/interfaces/r.py"
> sage -t "devel/sage/sage/quadratic_forms/
> quadratic_form__equivalence_testing.py"
> sage -t "devel/sage/sage/stats/test.py"
> sage -t "devel/sage/sage/stats/r.py
>
> I have a compilation on the same machine outside the chroot, and it
> works fine. Errors logs are below. Any suggestions would be
> appreciated!
>
> Thanks,
> Kay
>
> ----
>
> sage: r.version()
> ---------------------------------------------------------------------------
> RuntimeError Traceback (most recent call
> last)
>
> /home/sage/.sage/temp/bs0.bobsced.loc/27767/
> _home_sage__sage_init_sage_0.py in <module>()
>
> /home/sage/local/lib/python2.6/site-packages/sage/interfaces/r.pyc in
> version(self)
> 525 version_string_re = re.compile('^version.string\s*
> (R.*?)$', re.M)
> 526
> --> 527 s = self.eval('version')
> 528
> 529 major = int( major_re.findall(s)[0].strip() )
>
> /home/sage/local/lib/python2.6/site-packages/sage/interfaces/r.pyc in
> eval(self, code, globals, locals, synchronize, *args, **kwds)
> 974 # TODO split code at ";" outside of quotes and send
> them as individual
> 975 # lines without ";".
> --> 976 return Expect.eval(self, code,
> synchronize=synchronize, *args, **kwds)
> 977
> 978 def _r_to_sage_name(self, s):
>
> /home/sage/local/lib/python2.6/site-packages/sage/interfaces/
> expect.pyc in eval(self, code, strip, synchronize, locals, **kwds)
> 978 try:
> 979 with gc_disabled():
> --> 980 return '\n'.join([self._eval_line(L, **kwds)
> for L in code.split('\n') if L != ''])
> 981 except KeyboardInterrupt:
> 982 # DO NOT CATCH KeyboardInterrupt, as it is being
> caught
>
> /home/sage/local/lib/python2.6/site-packages/sage/interfaces/
> expect.pyc in _eval_line(self, line, allow_use_file, wait_for_prompt)
> 632 try:
> 633 if self._expect is None:
> --> 634 self._start()
> 635 E = self._expect
> 636 try:
>
> /home/sage/local/lib/python2.6/site-packages/sage/interfaces/r.pyc in
> _start(self)
> 302 sage: r._start()
> 303 """
> --> 304 Expect._start(self)
> 305
> 306 # width is line width, what's a good value? maximum is
> 10000!
>
> /home/sage/local/lib/python2.6/site-packages/sage/interfaces/
> expect.pyc in _start(self, alt_message, block_during_init)
> 467 self._session_number = BAD_SESSION
> 468 failed_to_start.append(self.__name)
> --> 469 raise RuntimeError, "Unable to start
> %s"%self.__name
> 470 self._expect.timeout = None
> 471 with gc_disabled():
>
> RuntimeError: Unable to start r
>
>
> sage -t "devel/sage/sage/interfaces/expect.py"
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 766:
> sage: r._sendstr('abc <- 10 +15;\n')
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_15[2]>", line 1, in <module>
> r._sendstr('abc <- 10 +15;\n')###line 766:
> sage: r._sendstr('abc <- 10 +15;\n')
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 866, in _sendstr
> self._start()
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> r.py", line 304, in _start
> Expect._start(self)
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 469, in _start
> raise RuntimeError, "Unable to start %s"%self.__name
> RuntimeError: Unable to start r
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 781:
> sage: w = walltime(t); w > 0.4 and w < 10
> Expected:
> True
> Got:
> False
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 788:
> sage: r._sendstr('abc;\n')
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_15[6]>", line 1, in <module>
> r._sendstr('abc;\n')###line 788:
> sage: r._sendstr('abc;\n')
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 866, in _sendstr
> self._start()
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> r.py", line 304, in _start
> Expect._start(self)
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 469, in _start
> raise RuntimeError, "Unable to start %s"%self.__name
> RuntimeError: Unable to start r
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 794:
> sage: r._expect_expr('25')
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_15[7]>", line 1, in <module>
> r._expect_expr('25')###line 794:
> sage: r._expect_expr('25')
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 814, in _expect_expr
> self._start()
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> r.py", line 304, in _start
> Expect._start(self)
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 469, in _start
> raise RuntimeError, "Unable to start %s"%self.__name
> RuntimeError: Unable to start r
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 800:
> sage: r._expect.before
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_15[8]>", line 1, in <module>
> r._expect.before###line 800:
> sage: r._expect.before
> AttributeError: 'NoneType' object has no attribute 'before'
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 855:
> sage: r._sendstr('a <- 10;\n')
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_16[2]>", line 1, in <module>
> r._sendstr('a <- 10;\n')###line 855:
> sage: r._sendstr('a <- 10;\n')
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 866, in _sendstr
> self._start()
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> r.py", line 304, in _start
> Expect._start(self)
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 469, in _start
> raise RuntimeError, "Unable to start %s"%self.__name
> RuntimeError: Unable to start r
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 856:
> sage: r.eval('a')
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_16[3]>", line 1, in <module>
> r.eval('a')###line 856:
> sage: r.eval('a')
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> r.py", line 976, in eval
> return Expect.eval(self, code, synchronize=synchronize, *args,
> **kwds)
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 980, in eval
> return '\n'.join([self._eval_line(L, **kwds) for L in
> code.split('\n') if L != ''])
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 634, in _eval_line
> self._start()
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> r.py", line 304, in _start
> Expect._start(self)
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 469, in _start
> raise RuntimeError, "Unable to start %s"%self.__name
> RuntimeError: Unable to start r
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 1753:
> sage: x = r([1,2,3]); x
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_54[2]>", line 1, in <module>
> x = r([Integer(1),Integer(2),Integer(3)]); x###line 1753:
> sage: x = r([1,2,3]); x
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 1042, in __call__
> raise TypeError, msg
> TypeError: Unable to start r
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 1755:
> sage: x.name()
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_54[3]>", line 1, in <module>
> x.name()###line 1755:
> sage: x.name()
> AttributeError: 'sage.symbolic.expression.Expression' object has
> no attribute 'name'
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 1757:
> sage: x = r([1,2,3]).name('x'); x
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_54[4]>", line 1, in <module>
> x = r([Integer(1),Integer(2),Integer(3)]).name('x'); x###line
> 1757:
> sage: x = r([1,2,3]).name('x'); x
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py", line 1042, in __call__
> raise TypeError, msg
> TypeError: Unable to start r
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/expect.py", line 1759:
> sage: x.name()
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compileflags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_54[5]>", line 1, in <module>
> x.name()###line 1759:
> sage: x.name()
> AttributeError: 'sage.symbolic.expression.Expression' object has
> no attribute 'name'
> **********************************************************************
> 3 items had failures:
> 5 of 10 in __main__.example_15
> 2 of 6 in __main__.example_16
> 4 of 9 in __main__.example_54
> ***Test Failed*** 11 failures.
> For whitespace errors, see the file /home/sage/tmp/.doctest_expect.py
> [8.2 s]
> exit code: 1024
>
>
> sage -t "devel/sage/sage/interfaces/r.py"
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 15:
> sage: x = r([10.4,5.6,3.1,6.4,21.7]); x
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compile
> flags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_0[2]>", line 1, in <module>
> x = r([RealNumber('10.4'),RealNumber('5.6'),RealNumber
> ('3.1'),RealNumber
> ('6.4'),RealNumber('21.7')]); x###line 15:
> sage: x = r([10.4,5.6,3.1,6.4,21.7]); x
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py"
> , line 1042, in __call__
> raise TypeError, msg
> TypeError: Unable to start r
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 20:
> sage: ~x
> Expected:
> [1] 0.09615385 0.17857143 0.32258065 0.15625000 0.04608295
> Got:
> 1/x
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 22:
> sage: 1/x
> Expected:
> [1] 0.09615385 0.17857143 0.32258065 0.15625000 0.04608295
> Got:
> 1/x
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 27:
> sage: y = r([x,0,x]); y
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compile
> flags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_0[5]>", line 1, in <module>
> y = r([x,Integer(0),x]); y###line 27:
> sage: y = r([x,0,x]); y
> File "/home/sage/local/lib/python/site-packages/sage/interfaces/
> expect.py"
> , line 1042, in __call__
> raise TypeError, msg
> TypeError: _interface_init_() takes exactly one argument (0 given)
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 35:
> sage: v = 2*x+y+1; v
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compile
> flags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_0[6]>", line 1, in <module>
> v = Integer(2)*x+y+Integer(1); v###line 35:
> sage: v = 2*x+y+1; v
> NameError: name 'y' is not defined
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 40:
> sage: sum(x)
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compile
> flags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_0[7]>", line 1, in <module>
> sum(x)###line 40:
> sage: sum(x)
> TypeError: 'sage.symbolic.expression.Expression' object is not
> iterable
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 42:
> sage: x.sum()
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compile
> flags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_0[8]>", line 1, in <module>
> x.sum()###line 42:
> sage: x.sum()
> AttributeError: 'sage.symbolic.expression.Expression' object has
> no attribut
> e 'sum'
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 46:
> sage: ((x-x.mean())^2/(x.length()-1)).sum()
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compile
> flags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_0[9]>", line 1, in <module>
> ((x-x.mean())**Integer(2)/(x.length()-Integer(1))).sum()
> ###line 46:
> sage: ((x-x.mean())^2/(x.length()-1)).sum()
> AttributeError: 'sage.symbolic.expression.Expression' object has
> no attribut
> e 'mean'
> **********************************************************************
> File "/home/sage/devel/sage/sage/interfaces/r.py", line 48:
> sage: x.var()
> Exception raised:
> Traceback (most recent call last):
> File "/home/sage/local/bin/ncadoctest.py", line 1231, in
> run_one_test
> self.run_one_example(test, example, filename, compileflags)
> File "/home/sage/local/bin/sagedoctest.py", line 38, in
> run_one_example
> OrigDocTestRunner.run_one_example(self, test, example,
> filename, compile
> flags)
> File "/home/sage/local/bin/ncadoctest.py", line 1172, in
> run_one_example
> compileflags, 1) in test.globs
> File "<doctest __main__.example_0[10]>", line 1, in <module>
> x.var()###line 48:
> sage: x.var()
> AttributeError: 'sage.symbolic.expression.Expression' object has
> no attribut
> e 'var'
> **********************************************************************
> etc...
>
> >
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