Sage 4.5.3.alpha2 released

30 views
Skip to first unread message

Mitesh Patel

unread,
Aug 23, 2010, 11:30:40 PM8/23/10
to sage-r...@googlegroups.com
Hi there,

We've released Sage 4.5.3.alpha2.

Source archive:

http://sage.math.washington.edu/home/release/sage-4.5.3.alpha2/sage-4.5.3.alpha2.tar

Upgrade path:

http://sage.math.washington.edu/home/release/sage-4.5.3.alpha2/sage-4.5.3.alpha2/

The long doctests pass for me on bsd, redhawk, sage, and
t2.math.washington.edu.

Please build, test, and report! We'd love to hear about your
experiences with this release.

The 4.5.3 series is still in feature freeze and blocker squeeze.


== Tickets ==

Closed tickets:

#7708: Harald Schilly: upgrade openopt spkg to 0.29 [Reviewed by Harald
Schilly]

Merged in sage-4.5.3.alpha2:

#9689: David Kirkby: Numerical noise on
devel/sage-main/sage/symbolic/expression.pyx computing sinh(1) [Reviewed
by John Cremona]
#9693: David Kirkby: Maxima is printing asinh(1.0) without a leading
zero (.8813735870195429) on Solaris 10 x86 [Reviewed by John Cremona]
#9703: David Kirkby: Doctest failures caused by non-working sympow on
32-bit Solaris x86 and 32-bit OpenSolaris [Reviewed by Jeroen Demeyer,
Mitesh Patel, Carl Witty]
#9722: Leif Leonhardy: PARI/GP build error on Fedora 13 [Reviewed by
Jeroen Demeyer, Mitesh Patel]
#9735: John Palmieri: Numerical noise on sage/stats/hmm/chmm.pyx on both
Solaris x86 and OpenSolaris x86 [Reviewed by David Kirkby]
#9760: John Palmieri: Possible numerical noise doctest failure in
sage/matrix/matrix2.pyx on t2 [Reviewed by David Kirkby]
#9761: David Kirkby: Adjust spkg/standard/deps to build Python before
zn_poly, and make two other dependencies explicit [Reviewed by Leif
Leonhardy]
#9765: John Palmieri: matrix2.pyx: replace "x < 1e-15" by "abs(x) <
1e-15" [Reviewed by Mitesh Patel]

Marshall Hampton

unread,
Aug 24, 2010, 1:13:53 AM8/24/10
to sage-release
All standard tests passed on 64-bit Ubuntu 9.10, cpu is a i7 860, on
an upgrade from 4.5.3.alpha1.

-Marshall

Alex Ghitza

unread,
Aug 24, 2010, 3:34:50 AM8/24/10
to Mitesh Patel, sage-r...@googlegroups.com
On Mon, 23 Aug 2010 22:30:40 -0500, Mitesh Patel <qed...@gmail.com> wrote:
> Please build, test, and report! We'd love to hear about your
> experiences with this release.

Upgraded from 4.5.1 (I think) and passed long tests on

[aghitza@soleil sage-4.5.1]$ uname -a
Linux soleil.ms.unimelb.edu.au 2.6.18-194.11.1.el5 #1 SMP Tue Jul 27 05:45:06 EDT 2010 x86_64 x86_64 x86_64 GNU/Linux

Best,
Alex


--
Alex Ghitza -- http://aghitza.org/
Lecturer in Mathematics -- The University of Melbourne -- Australia

Rob Beezer

unread,
Aug 24, 2010, 12:10:15 PM8/24/10
to sage-release
Built from scratch, passes all tests with

export MAKE="make -j4"
export SAGE_PARALLEL_SPKG_BUILD="yes"
make ptestlong

on

(a) 64-bit KUbuntu 10.04 on Intel CoreDuo
(b) 64-bit Ubuntu 10.04 on Intel i7-620M

Rob

kcrisman

unread,
Aug 24, 2010, 1:11:35 PM8/24/10
to sage-release
Upgraded fine, passed all normal tests (except my issue with _imaging
which is not relevant), from alpha1 on Mac OS X 10.6.

- kcrisman

georg grafendorfer

unread,
Aug 24, 2010, 1:57:28 PM8/24/10
to sage-release
Hi,

AMD Phenom X4 II, Fedora 13

build fine,

one doctest error after:

make ptestlong

The following tests failed:

sage -t -long devel/sage/sage/all.py # 0 doctests failed
sage -t -long devel/sage/sage/all_cmdline.py # 0 doctests failed
sage -t -long devel/sage/sage/interfaces/r.py # 1 doctests failed
----------------------------------------------------------------------
Total time for all tests: 2373.4 seconds



sage -t -long devel/sage/sage/interfaces/r.py
**********************************************************************
File "/scratch/sage-4.5.3.alpha2/devel/sage-main/sage/interfaces/
r.py", line 999:
sage: r.library("lattice")
Exception raised:
Traceback (most recent call last):
File "/scratch/sage-4.5.3.alpha2/local/bin/ncadoctest.py", line
1231, in run_one_test
self.run_one_example(test, example, filename, compileflags)
File "/scratch/sage-4.5.3.alpha2/local/bin/sagedoctest.py", line
38, in run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compileflags)
File "/scratch/sage-4.5.3.alpha2/local/bin/ncadoctest.py", line
1172, in run_one_example
compileflags, 1) in test.globs
File "<doctest __main__.example_37[7]>", line 1, in <module>
r.library("lattice")###line 999:
sage: r.library("lattice")
File "/scratch/sage-4.5.3.alpha2/local/lib/python/site-packages/
sage/interfaces/r.py", line 574, in library
raise ImportError, "%s"%ret
ImportError: Loading required package: lattice
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE,
logical.return = TRUE, :
there is no package called 'lattice'
**********************************************************************
1 items had failures:
1 of 8 in __main__.example_37
***Test Failed*** 1 failures.
For whitespace errors, see the file /u/ggeorg/.sage//tmp/.doctest_r.py
[6.3 s]

Georg

leif

unread,
Aug 24, 2010, 2:15:24 PM8/24/10
to sage-r...@googlegroups.com
Mitesh Patel wrote:
> We've released Sage 4.5.3.alpha2.
>
> Source archive:
>
> http://sage.math.washington.edu/home/release/sage-4.5.3.alpha2/sage-4.5.3.alpha2.tar
>
> Upgrade path:
>
> http://sage.math.washington.edu/home/release/sage-4.5.3.alpha2/sage-4.5.3.alpha2/
>
> The long doctests pass for me on bsd, redhawk, sage, and
> t2.math.washington.edu.
>
> Please build, test, and report! We'd love to hear about your
> experiences with this release.
>
> The 4.5.3 series is still in feature freeze and blocker squeeze.

Ubuntu 9.04 x86_64 (Core2, gcc 4.5.0, native code, O3):

make build: OK (parallel build from scratch, 32 jobs)
make doc: OK
make ptestlong: OK (all tests passed; 4 threads)


Fedora 13 x86_64 (Core2, gcc 4.4.4, native code, O3):

make build: OK (parallel build from scratch, 32 jobs)
make doc: OK
make ptestlong: OK (all tests passed; 4 threads)


Ubuntu 9.04 x86 (Pentium 4 Prescott, gcc 4.3.3, native code):

make build: OK (parallel build from scratch, 6 jobs)
make doc: OK
make ptestlong: OK (all tests passed; 2 threads)


-Leif

David Kirkby

unread,
Aug 24, 2010, 2:17:39 PM8/24/10
to sage-r...@googlegroups.com
On 24 August 2010 18:57, georg grafendorfer

<georg.gra...@gmail.com> wrote:
> Hi,
>
> AMD Phenom X4 II, Fedora 13
>
> build fine,
>
> one doctest error after:
>
> make ptestlong
>
> The following tests failed:
>
>        sage -t  -long devel/sage/sage/all.py # 0 doctests failed
>        sage -t  -long devel/sage/sage/all_cmdline.py # 0 doctests failed
>        sage -t  -long devel/sage/sage/interfaces/r.py # 1 doctests failed
> ----------------------------------------------------------------------
> Total time for all tests: 2373.4 seconds

We need to sort out these test that fail with zero failures, like the
first two you list do.

Dave

Justin C. Walker

unread,
Aug 24, 2010, 2:29:02 PM8/24/10
to sage-r...@googlegroups.com

On Aug 23, 2010, at 20:30 , Mitesh Patel wrote:

Upgraded from 4.5.3.a1, w/o problems. Ran 'ptestlong', and one test
failed. Failure noted below. I reran the test by hand and it
passed. Mac OS X, 10.5.8, Dual Quad Xeon.

Justin


sage -t -long devel/sage/sage/interfaces/psage.py
**********************************************************************
File "/Users/Sage/sage-4.5.3.alpha1/devel/sage-main/sage/interfaces/
psage.py", l
ine 35:
sage: print "ignore this"; w # random output


Exception raised:
Traceback (most recent call last):

File "/Users/Sage/sage-4.5.3.alpha1/local/bin/ncadoctest.py",
line 1231, i


n run_one_test
self.run_one_example(test, example, filename, compileflags)

File "/Users/Sage/sage-4.5.3.alpha1/local/bin/sagedoctest.py",

line 38, in
run_one_example
OrigDocTestRunner.run_one_example(self, test, example,
filename, compile
flags)

File "/Users/Sage/sage-4.5.3.alpha1/local/bin/ncadoctest.py",
line 1172, i


n run_one_example
compileflags, 1) in test.globs

File "<doctest __main__.example_0[5]>", line 1, in <module>
print "ignore this"; w # random output###line 35:
sage: print "ignore this"; w # random output
File "/Users/Sage/sage-4.5.3.alpha1/local/lib/python/site-
packages/sage/mi
sc/displayhook.py", line 174, in displayhook
print_obj(sys.stdout, obj)
File "/Users/Sage/sage-4.5.3.alpha1/local/lib/python/site-
packages/sage/mi
sc/displayhook.py", line 142, in print_obj
print >>out_stream, `obj`
File "/Users/Sage/sage-4.5.3.alpha1/local/lib/python/site-
packages/sage/in
terfaces/expect.py", line 1670, in __repr__
s = s.replace(self._name, self.__dict__['__custom_name'])
KeyError: '__custom_name'

--
Justin C. Walker, Curmudgeon at Large
Institute for the Absorption of Federal Funds
-----------
I'm beginning to like the cut of his jibberish.
-----------

Dr. David Kirkby

unread,
Aug 24, 2010, 8:14:55 PM8/24/10
to sage-r...@googlegroups.com
On 08/24/10 07:29 PM, Justin C. Walker wrote:
>
> On Aug 23, 2010, at 20:30 , Mitesh Patel wrote:
>
>> Hi there,
>>
>> We've released Sage 4.5.3.alpha2.
>>
>> Source archive:
>>
>> http://sage.math.washington.edu/home/release/sage-4.5.3.alpha2/sage-4.5.3.alpha2.tar
>>
>>
>> Upgrade path:
>>
>> http://sage.math.washington.edu/home/release/sage-4.5.3.alpha2/sage-4.5.3.alpha2/
>>
>
> Upgraded from 4.5.3.a1, w/o problems. Ran 'ptestlong', and one test
> failed. Failure noted below. I reran the test by hand and it passed. Mac
> OS X, 10.5.8, Dual Quad Xeon.
>
> Justin

Can you think of any reason the test might have failed first time? Do your logs
show a lack or swap space, disk I/O error, or something else that might explain
why it failed first time, but passed when you re-run it?

I find this a bit worrying, as we don't know if Sage is getting things wrong
occasionally, or the doctest framework is broken. But this seems quite a common
problem, with tests failing in ptestlong but passing individually.

What I don't know for sure is if testlong is more reliable. I think it might be.

Dave

Justin C. Walker

unread,
Aug 24, 2010, 9:29:27 PM8/24/10
to sage-r...@googlegroups.com

The only things of note in the logs during the time of the tests were
three crashes, 2 in maxima, one in genus2reduction. Not sure how to
tie the psage failure to one of those. It looks like there is perhaps
a problem related to string matching, if I understand the traceback.
I know squat about this stuff, so I can only speculate wildly and
inaccurately.

The '__custom_name' key is checked by hasattr() before being
referenced in the line that blows up (with a KeyError exception).
That seems quite odd to me.

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Enhancement of the Director's Income
--------
Experience is what you get
when you don't get what you want.
--------

Mitesh Patel

unread,
Aug 24, 2010, 9:57:42 PM8/24/10
to sage-r...@googlegroups.com
On 08/24/2010 08:29 PM, Justin C. Walker wrote:
> On Aug 24, 2010, at 17:14 , Dr. David Kirkby wrote:
>> On 08/24/10 07:29 PM, Justin C. Walker wrote:
>>> Upgraded from 4.5.3.a1, w/o problems. Ran 'ptestlong', and one test
>>> failed. Failure noted below. I reran the test by hand and it passed. Mac
>>> OS X, 10.5.8, Dual Quad Xeon.
>>
>> Can you think of any reason the test might have failed first time? Do
>> your logs show a lack or swap space, disk I/O error, or something else
>> that might explain why it failed first time, but passed when you
>> re-run it?
>>
>> I find this a bit worrying, as we don't know if Sage is getting things
>> wrong occasionally, or the doctest framework is broken. But this seems
>> quite a common problem, with tests failing in ptestlong but passing
>> individually.
>
> The only things of note in the logs during the time of the tests were
> three crashes, 2 in maxima, one in genus2reduction. Not sure how to tie
> the psage failure to one of those. It looks like there is perhaps a
> problem related to string matching, if I understand the traceback. I
> know squat about this stuff, so I can only speculate wildly and
> inaccurately.
>
> The '__custom_name' key is checked by hasattr() before being referenced
> in the line that blows up (with a KeyError exception). That seems quite
> odd to me.

Could you give a link to the ptestlong log?

Mitesh Patel

unread,
Aug 24, 2010, 10:32:33 PM8/24/10
to sage-r...@googlegroups.com


It seems that R's lattice package wasn't compiled or installed on your
system. Could you confirm this by rerunning the test and checking the
output of

$ cd SAGE_ROOT
$ ./sage -R
[...]
> installed.packages()

? On bsd (OS X 10.6) and sage.math (Ubuntu 8.04.4 LTS), this gives
information for 27 packages:

base
boot
class
cluster
codetools
datasets
foreign
graphics
grDevices
grid
KernSmooth
lattice
MASS
Matrix
methods
mgcv
nlme
nnet
rpart
spatial
splines
stats
stats4
survival
tcltk
tools
utils

On t2.math (Solaris 10), I get data for 20 packages:

base
boot
cluster
codetools
datasets
foreign
graphics
grDevices
grid
KernSmooth
lattice
MASS
methods
nlme
splines
stats
stats4
tcltk
tools
utils

This is a known problem on t2, at least:

http://trac.sagemath.org/sage_trac/ticket/9201

Justin C. Walker

unread,
Aug 24, 2010, 10:34:06 PM8/24/10
to sage-r...@googlegroups.com

On Aug 24, 2010, at 18:57 , Mitesh Patel wrote:

> On 08/24/2010 08:29 PM, Justin C. Walker wrote:
>> On Aug 24, 2010, at 17:14 , Dr. David Kirkby wrote:
>>> On 08/24/10 07:29 PM, Justin C. Walker wrote:

[snip]


>> The '__custom_name' key is checked by hasattr() before being
>> referenced
>> in the line that blows up (with a KeyError exception). That seems
>> quite
>> odd to me.
>
> Could you give a link to the ptestlong log?

The log is at
sage.math.washington.edu:~justin/logs/4.5.3.a2.log

Justin

--
Justin C. Walker
Curmudgeon-at-large
--
Network, n., Difference between work
charged for and work done

Jeroen Demeyer

unread,
Aug 25, 2010, 2:27:59 AM8/25/10
to sage-r...@googlegroups.com
Built and passed all tests (testlong) on a PPC Mac OSX 10.4 with gcc-4.0.1

Jeroen.

georg grafendorfer

unread,
Aug 25, 2010, 9:39:34 AM8/25/10
to sage-release
if I do this I get an output of more than 10000! lines, the word
'lattices' do appear sometimes, here is a filtered version of the
output with only lines where 'lattice' appears:

EngrExpt "R (>= 2.9.0), lattice"
HH "R (>= 2.5.0), lattice, stats, grid, multcomp
(>= 1.1-2),\nmvtnorm, methods, leaps"
HSAUR "R (>= 2.2.0), lattice, MASS, scatterplot3d (>=
0.3-23)"
ICEinfer "R (>= 2.5.0), lattice"
MIfuns "lattice, MASS, methods, reshape"
NRAIA "lattice, stats"
PKtools "methods, lattice, nlme, R2HTML, xtable"
RGraphics "R (>= 2.0.0), grDevices, graphics, grid,
lattice"
USPS "R (>= 1.8.0), cluster, lattice, gss"
adaptTest "lattice"
agsemisc "R (>= 1.8.0), lattice, grid"
asuR "MASS, lattice, grid, methods, lme4"
binom "lattice"
chplot "ellipse, KernSmooth, lattice"
dprep "MASS, nnet, lattice, class"
effects "R (>= 2.4.0), lattice, grid, MASS, nnet,
colorspace"
hydrosanity "R (>= 2.5.0), playwith (>= 0.8.24), lattice (>=
0.16)"
influence.ME "lme4, lattice"
irtProb "R (>= 2.0.0), lattice, methods, stats, moments"
kinship "methods, survival, nlme, lattice, R (>= 2.8.0)"
kzs "R (>= 2.8.0), graphics, lattice, stats"
ldbounds "lattice"
mapLD "R (>= 2.4.1), lattice"
mixPHM "survival, lattice"
mixstock "coda, plotrix, abind, lattice"
primer "deSolve, lattice"
qtlbim "stats, qtl (>= 1.9.43), lattice, coda, tools,
MASS"
scape "R (>= 2.1.1), gdata, grid, Hmisc, lattice"
scapeMCMC "R (>= 2.1.1), coda, gdata, gplots, grid,
gtools, lattice"
sda "R (>= 2.7.0), lattice, entropy (>= 1.1.3),
corpcor (>= 1.5.2),\nfdrtool (>= 1.2.5)"
lga "boot, lattice"
nlme "lattice"
CombMSC "lattice, rgl"
SMIR "lattice, foreign, gdata, car, dglm, gnm, MASS,
npmlreg,\nsurvival"
STAR "lattice, HiddenMarkov, snow, rstream"
beanplot "vioplot, lattice"
npmlreg "MASS, forward, nlme, lattice"
psyphy "MASS, nlme, lattice"
grid "lattice"

Georg

kcrisman

unread,
Aug 25, 2010, 12:44:47 PM8/25/10
to sage-release
Whoah!
Are you sure you didn't type something else? This seems to indicate
you have nearly every optional package there is installed! It also
seems to indicate that all these packages (which depend on lattice
graphics) are installed... which shouldn't happen if lattice fails to
install.

Can you try reinstalling the R package with

./sage -f r

?

georg grafendorfer

unread,
Aug 25, 2010, 3:32:30 PM8/25/10
to sage-release



> Are you sure you didn't type something else? This seems to indicate
> you have nearly every optional package there is installed!  It also
> seems to indicate that all these packages (which depend on lattice
> graphics) are installed... which shouldn't happen if lattice fails to
> install.
>
> Can you try reinstalling the R package with
>
> ./sage -f r
>

I recompiled R with
./sage -f r

but still the same:

ggeorg@maschke% ./sage -R

R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

Loading required package: utils
extending .libPaths() R-version specific library ...
Inserting before position 1 ..
library ‘/usr/local64.sfs/app/R/R_local/library_FC13’ with no packages
*not* added to lib path
Attaching package of SfS goodies..
Error in library(sfsmisc, keep.source = TRUE) :
there is no package called 'sfsmisc'
In addition: Warning messages:
1: In libPIns(biocLibrary, beforeLib = file.path(RrootDir,
"library"), :
/usr/local64.sfs/app/R/Bioconductor/library_2.5_FC13 is not an
existing directory
2: In libPIns(nlib = file.path(RrootDir, paste("library",
R.maj.ver(), :
.libPaths() contains no entries matching ‘/usr/local64.sfs/app/R/
R_local/library$’
> installed.packages()
Package
ADGofTest "ADGofTest"
AIGIS "AIGIS"
AIS "AIS"
ALS "ALS"
AcceptanceSampling "AcceptanceSampling"
AdMit "AdMit"
AdaptFit "AdaptFit"
Animal "Animal"
ArDec "ArDec"
.........
.........


there is an error message about missing packages when starting R with
./sage -R

Georg

Mitesh Patel

unread,
Aug 25, 2010, 6:27:15 PM8/25/10
to sage-r...@googlegroups.com
On 08/24/2010 01:29 PM, Justin C. Walker wrote:
> Upgraded from 4.5.3.a1, w/o problems. Ran 'ptestlong', and one test
> failed. Failure noted below. I reran the test by hand and it passed.
> Mac OS X, 10.5.8, Dual Quad Xeon.
>
> sage -t -long devel/sage/sage/interfaces/psage.py


The PSage interface spawns multiple parallel, non-blocking copies of the
Sage interpreter. The problem *might* be a race condition within
psage.py itself that the doctest occasionally exposes.


> **********************************************************************
> File
> "/Users/Sage/sage-4.5.3.alpha1/devel/sage-main/sage/interfaces/psage.py", l

Justin also wrote:
> The '__custom_name' key is checked by hasattr() before being referenced
> in the line that blows up (with a KeyError exception). That seems quite
> odd to me.


From sage.interfaces.expect.ExpectElement:

def __repr__(self):
self._check_valid()
try:
if self._get_using_file:
s = self.parent().get_using_file(self._name)
except AttributeError:
s = self.parent().get(self._name)
if s.__contains__(self._name):
if hasattr(self, '__custom_name'):


s = s.replace(self._name, self.__dict__['__custom_name'])

return s

Does anyone have an example for which the replace statement is executed?

Mitesh Patel

unread,
Aug 25, 2010, 6:49:18 PM8/25/10
to sage-r...@googlegroups.com
> library �/usr/local64.sfs/app/R/R_local/library_FC13� with no packages

> *not* added to lib path
> Attaching package of SfS goodies..
> Error in library(sfsmisc, keep.source = TRUE) :
> there is no package called 'sfsmisc'
> In addition: Warning messages:
> 1: In libPIns(biocLibrary, beforeLib = file.path(RrootDir,
> "library"), :
> /usr/local64.sfs/app/R/Bioconductor/library_2.5_FC13 is not an
> existing directory
> 2: In libPIns(nlib = file.path(RrootDir, paste("library",
> R.maj.ver(), :
> .libPaths() contains no entries matching �/usr/local64.sfs/app/R/
> R_local/library$�


Is is possible that Sage's R is reading a system-wide/personal R
configuration file with these paths?

For reference, on {bsd,sage,t2}.math I see

$ sage -R

R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.


Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>


Justin C. Walker

unread,
Aug 25, 2010, 7:08:32 PM8/25/10
to sage-r...@googlegroups.com

On Aug 25, 2010, at 15:27 , Mitesh Patel wrote:

> On 08/24/2010 01:29 PM, Justin C. Walker wrote:
>> Upgraded from 4.5.3.a1, w/o problems. Ran 'ptestlong', and one test
>> failed. Failure noted below. I reran the test by hand and it
>> passed.
>> Mac OS X, 10.5.8, Dual Quad Xeon.
>>
>> sage -t -long devel/sage/sage/interfaces/psage.py
>
>
> The PSage interface spawns multiple parallel, non-blocking copies of
> the
> Sage interpreter. The problem *might* be a race condition within
> psage.py itself that the doctest occasionally exposes.

Someone who knows what's going on in this code will have to speak up.
I would expect the code here to be executed for each
"thread" (although I think that's not exactly what's going on under
the covers). Isn't 'self' a single instance of something or other
(pardon my drifting into technical speak)?

> Justin also wrote:
>> The '__custom_name' key is checked by hasattr() before being
>> referenced
>> in the line that blows up (with a KeyError exception). That seems
>> quite
>> odd to me.
>
>
> From sage.interfaces.expect.ExpectElement:
>
> def __repr__(self):
> self._check_valid()
> try:
> if self._get_using_file:
> s = self.parent().get_using_file(self._name)
> except AttributeError:
> s = self.parent().get(self._name)
> if s.__contains__(self._name):
> if hasattr(self, '__custom_name'):
> s = s.replace(self._name,
> self.__dict__['__custom_name'])
> return s
>
> Does anyone have an example for which the replace statement is
> executed?

Isn't the blow-up an instance of the statement being executed? Am I
missing your point?

Justin

--
Justin C. Walker, Curmudgeon-At-Large
Institute for the Enhancement of the Director's Income
--------

When LuteFisk is outlawed,
Only outlaws will have LuteFisk
--------

Anthony David

unread,
Aug 25, 2010, 7:14:52 PM8/25/10
to sage-r...@googlegroups.com
On Tue, Aug 24, 2010 at 1:30 PM, Mitesh Patel <qed...@gmail.com> wrote:
Hi there,

We've released Sage 4.5.3.alpha2.

Source archive:

http://sage.math.washington.edu/home/release/sage-4.5.3.alpha2/sage-4.5.3.alpha2.tar

Upgrade path:

http://sage.math.washington.edu/home/release/sage-4.5.3.alpha2/sage-4.5.3.alpha2/

The long doctests pass for me on bsd, redhawk, sage, and
t2.math.washington.edu.

Please build, test, and report!  We'd love to hear about your
experiences with this release.

The 4.5.3 series is still in feature freeze and blocker squeeze.



Notebook() failed to start

build succeeded.
Build finished.  The built documents can be found in /home/adavid/build/sage-4.5.3.alpha2/devel/sage/doc/output/html/fr/a_tour_of_sage

uname -a
Linux carbonate 2.6.32-24-generic #39-Ubuntu SMP Wed Jul 28 05:14:15 UTC 2010 x86_64 GNU/Linux

ii  kde-window-manager      4:4.4.2-0ubuntu14       the KDE 4 window manager (KWin)


adavid@carbonate:~/build/sage-4.5.3.alpha2$ ./sage
----------------------------------------------------------------------
| Sage Version 4.5.3.alpha2, Release Date: 2010-08-23                |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------
**********************************************************************
*                                                                    *
* Warning: this is a prerelease version, and it may be unstable.     *
*                                                                    *
**********************************************************************
sage: notebook()
The notebook files are stored in: sage_notebook.sagenb
Removing stale pidfile sage_notebook.sagenb/twistd.pid
**************************************************
*                                                *
* Open your web browser to http://localhost:8000 *
*                                                *
**************************************************
2010-08-26 09:05:53+1000 [-] Log opened.
2010-08-26 09:05:53+1000 [-] twistd 9.0.0 (/home/adavid/build/sage-4.5.3.alpha2/local/bin/python 2.6.4) starting up.
2010-08-26 09:05:53+1000 [-] reactor class: twisted.internet.selectreactor.SelectReactor.
2010-08-26 09:05:53+1000 [-] twisted.web2.channel.http.HTTPFactory starting on 8000
2010-08-26 09:05:53+1000 [-] Starting factory <twisted.web2.channel.http.HTTPFactory instance at 0x3f19b48>
<unknown program name>(27171)/ ClientApp::doIt: Creating ClientApp
kioclient(27171) ClientApp::kde_open: KUrl("http://localhost:8000/?startup_token=ec21c2efc9000116f3227c583804d5d3")
kioclient(27171) KSharedUiServerProxy::KSharedUiServerProxy: kuiserver registered
test: 448: Illegal number:
test: 448: Illegal number:
test: 448: Illegal number:
2010-08-26 09:06:00+1000 [HTTPChannel,1,127.0.0.1] /home/adavid/build/sage-4.5.3.alpha2/local/lib/python2.6/site-packages/Twisted-9.0.0-py2.6-linux-x86_64.egg/twisted/internet/defer.py:262: exceptions.DeprecationWarning: Don't pass strings (like 'Bad token') to failure.Failure (replacing with a DefaultException).
2010-08-26 09:06:00+1000 [HTTPChannel,1,127.0.0.1] Exception rendering:
2010-08-26 09:06:00+1000 [HTTPChannel,1,127.0.0.1] Unhandled Error

        Traceback (most recent call last):
        Failure: twisted.python.failure.DefaultException: Bad token


 
== Tickets ==

Closed tickets:

#7708: Harald Schilly: upgrade openopt spkg to 0.29 [Reviewed by Harald
Schilly]

Merged in sage-4.5.3.alpha2:

#9689: David Kirkby: Numerical noise on
devel/sage-main/sage/symbolic/expression.pyx computing sinh(1) [Reviewed
by John Cremona]
#9693: David Kirkby: Maxima is printing asinh(1.0) without a leading
zero (.8813735870195429) on Solaris 10 x86 [Reviewed by John Cremona]
#9703: David Kirkby: Doctest failures caused by non-working sympow on
32-bit Solaris x86 and  32-bit OpenSolaris [Reviewed by Jeroen Demeyer,
Mitesh Patel, Carl Witty]
#9722: Leif Leonhardy: PARI/GP build error on Fedora 13 [Reviewed by
Jeroen Demeyer, Mitesh Patel]
#9735: John Palmieri: Numerical noise on sage/stats/hmm/chmm.pyx on both
Solaris x86 and OpenSolaris x86 [Reviewed by David Kirkby]
#9760: John Palmieri: Possible numerical noise doctest failure in
sage/matrix/matrix2.pyx on t2 [Reviewed by David Kirkby]
#9761: David Kirkby: Adjust spkg/standard/deps to build Python before
zn_poly, and make two other dependencies explicit [Reviewed by Leif
Leonhardy]
#9765: John Palmieri: matrix2.pyx: replace "x < 1e-15" by "abs(x) <
1e-15" [Reviewed by Mitesh Patel]

--
You received this message because you are subscribed to the Google Groups "sage-release" group.
To post to this group, send email to sage-r...@googlegroups.com.
To unsubscribe from this group, send email to sage-release...@googlegroups.com.
For more options, visit this group at http://groups.google.com/group/sage-release?hl=en.


Mitesh Patel

unread,
Aug 25, 2010, 8:46:08 PM8/25/10
to sage-r...@googlegroups.com


Does the problem recur if you try again with 'notebook()' or use
'notebook(open_viewer=False)' and manually browse to http://localhost:8000 ?

Anthony David

unread,
Aug 25, 2010, 9:18:24 PM8/25/10
to sage-r...@googlegroups.com

Works OK with the manual browse.


sage: notebook(open_viewer=False)

The notebook files are stored in: sage_notebook.sagenb
**************************************************
*                                                *
* Open your web browser to http://localhost:8000 *
*                                                *
**************************************************
2010-08-26 11:15:56+1000 [-] Log opened.
2010-08-26 11:15:56+1000 [-] twistd 9.0.0 (/home/adavid/build/sage-4.5.3.alpha2/local/bin/python 2.6.4) starting up.
2010-08-26 11:15:56+1000 [-] reactor class: twisted.internet.selectreactor.SelectReactor.
2010-08-26 11:15:56+1000 [-] twisted.web2.channel.http.HTTPFactory starting on 8000
2010-08-26 11:15:56+1000 [-] Starting factory <twisted.web2.channel.http.HTTPFactory instance at 0x51eab48>

2010-08-26 11:16:21+1000 [HTTPChannel,1,127.0.0.1] User 'admin' logged in.


leif

unread,
Aug 26, 2010, 4:18:29 AM8/26/10
to sage-r...@googlegroups.com
Mitesh Patel wrote:
> We've released Sage 4.5.3.alpha2.
>
> [...]

>
> Please build, test, and report! We'd love to hear about your
> experiences with this release.
>
> The 4.5.3 series is still in feature freeze and blocker squeeze.
>
> [...]

Ubuntu 10.04 LTS x86_64 (Core2, gcc 4.4.3, native code, O3):

make build: OK (parallel build from scratch, 32 jobs)
make doc: OK
make ptestlong: OK (all tests passed; 4 threads)


Fedora 13 x86 (Pentium 4 Prescott, gcc 4.4.4, native code, O3):

Mitesh Patel

unread,
Aug 26, 2010, 5:25:29 AM8/26/10
to sage-r...@googlegroups.com
On 08/25/2010 08:18 PM, Anthony David wrote:

It appears to be a KDE configuration problem. Which Linux distribution
and version are you running? Perhaps someone who runs Sage on the same
or a similar distribution can provide additional data? Unfortunately, I
don't have access to a machine with both Sage and KDE.

Another workaround is to

export SAGE_BROWSER="/usr/bin/firefox"

say, before starting Sage.

Another example:

export SAGE_BROWSER='~/bin/Sage_browser'

where Sage_browser is an executable script that contains

#!/bin/bash
/usr/bin/firefox -P myprofile -remote "openURL($*, new-tab)"

This should open the requested page in a new tab in an already running
Firefox profile called myprofile.

Tim Joseph Dumol

unread,
Aug 26, 2010, 6:51:33 AM8/26/10
to sage-r...@googlegroups.com
I have experienced this problem before. Setting SAGE_BROWSER to your
preferred browser is the best way to fix this, as Mitesh Patel
suggested.

> --
> You received this message because you are subscribed to the Google Groups "sage-release" group.
> To post to this group, send email to sage-r...@googlegroups.com.
> To unsubscribe from this group, send email to sage-release...@googlegroups.com.
> For more options, visit this group at http://groups.google.com/group/sage-release?hl=en.
>
>

--
Tim Joseph Dumol <tim (at) timdumol (dot) com>
http://timdumol.com

leif

unread,
Aug 26, 2010, 8:03:29 AM8/26/10
to sage-r...@googlegroups.com
Mitesh Patel wrote:
> On 08/25/2010 08:18 PM, Anthony David wrote:
>> On Thu, Aug 26, 2010 at 10:46 AM, Mitesh Patel wrote:
>> On 08/25/2010 06:14 PM, Anthony David wrote:
>> > Notebook() failed to start
>> >
>> > build succeeded.
>> > Build finished. The built documents can be found in
>> > /home/adavid/build/sage-4.5.3.alpha2/devel/sage/doc/output/html/fr/a_tour_of_sage
>> >
>> > uname -a
>> > Linux carbonate 2.6.32-24-generic #39-Ubuntu SMP Wed Jul 28
>> 05:14:15 UTC
>> > 2010 x86_64 GNU/Linux
>> >
>> > ii kde-window-manager 4:4.4.2-0ubuntu14 the KDE 4 window
>> > manager (KWin)
>> >
>> > [...]

>>
>> Does the problem recur if you try again with 'notebook()' or use
>> 'notebook(open_viewer=False)' and manually browse to
>> http://localhost:8000 ?
>>
>> Works OK with the manual browse.
>
> It appears to be a KDE configuration problem. Which Linux distribution
> and version are you running?

Proxy answer:

[K]Ubuntu 10.04 LTS amd64 (x86_64, i.e. 64-bit).


-Leif

Mitesh Patel

unread,
Aug 26, 2010, 5:22:47 PM8/26/10
to sage-r...@googlegroups.com
On 08/25/2010 06:08 PM, Justin C. Walker wrote:
> On Aug 25, 2010, at 15:27 , Mitesh Patel wrote:
>> On 08/24/2010 01:29 PM, Justin C. Walker wrote:
>> Justin also wrote:
>>> The '__custom_name' key is checked by hasattr() before being referenced
>>> in the line that blows up (with a KeyError exception). That seems quite
>>> odd to me.
>>
>> From sage.interfaces.expect.ExpectElement:
>>
>> def __repr__(self):
>> self._check_valid()
>> try:
>> if self._get_using_file:
>> s = self.parent().get_using_file(self._name)
>> except AttributeError:
>> s = self.parent().get(self._name)
>> if s.__contains__(self._name):
>> if hasattr(self, '__custom_name'):
>> s = s.replace(self._name, self.__dict__['__custom_name'])
>> return s
>>
>> Does anyone have an example for which the replace statement is executed?
>
> Isn't the blow-up an instance of the statement being executed? Am I
> missing your point?


I should have been clearer. I'm looking for other, working examples
with which to experiment and to write doctests for
ExpectElement.__repr__. With

if s.__contains__(self._name):
print 'FOOO self._name', self._name
if hasattr(self, '__custom_name'):
print 'FOOO self.__custom_name', self.__custom_name


s = s.replace(self._name, self.__dict__['__custom_name'])

the long doctests still pass for me on sage.math.

Also, I ran

./sage -t -long devel/sage/sage/interfaces/psage.py

serially 1000 times in each of 20 copies of 4.5.3.alpha1, each with its
own DOT_SAGE directory. There were 17 failures, all the same as on your
system, out of 20000 total runs.

This appears to rule out the Sage parallel doctester
SAGE_LOCAL/bin/sage-ptest as the source of the problem.

I'm now batch-testing a .sage file that contains just the psage.py example

v = [PSage() for _ in range(3)]
w = [x('factor(2^%s-1)'% randint(250,310)) for x in v]
w # random output (depends on timing)
w # random output

Anthony David

unread,
Aug 26, 2010, 5:28:02 PM8/26/10
to sage-r...@googlegroups.com

Ubuntu 10.04.1

The workaround is sufficient at this stage. I have only just started using KDE as an experiment.

Thanks

Anthony
 
Another workaround is to

export SAGE_BROWSER="/usr/bin/firefox"

say, before starting Sage.

Another example:

export SAGE_BROWSER='~/bin/Sage_browser'

where Sage_browser is an executable script that contains

#!/bin/bash
/usr/bin/firefox -P myprofile -remote "openURL($*, new-tab)"

This should open the requested page in a new tab in an already running
Firefox profile called myprofile.

Rob Beezer

unread,
Aug 26, 2010, 10:16:41 PM8/26/10
to sage-release
On Aug 26, 2:28 pm, Anthony David <ajdavi...@gmail.com> wrote:
> The workaround is sufficient at this stage. I have only just started using
> KDE as an experiment.

KDE likes to default to Konqueror to handle various browser tasks,
especially when you are in some other KDE application.

Though Sage is not part of KDE, the notebook startup seems to find
Konqueror and then chokes on the automated login of the admin user
(IIRC).

As others have said already, setting SAGE_BROWSER works well long
term, and short-term you can just start Firefox and use the right
localhost URL to connect.

Rob

Justin C. Walker

unread,
Aug 26, 2010, 10:21:20 PM8/26/10
to sage-r...@googlegroups.com

On Aug 23, 2010, at 20:30 , Mitesh Patel wrote:

> Hi there,
>


> We've released Sage 4.5.3.alpha2.
>

Upgraded from 4.5.3.a1 w/o problems. All tests passed, with this
command:
$ SAGE_PARALLEL_SPKG_BUILD=yes SAGE64=yes MAKE="make -j3" make
ptestlong
Mac OS X, 10.6.4, Core i7.

Justin

--
Justin C. Walker, Curmudgeon-At-Large, Director


Institute for the Enhancement of the Director's Income
--------

The path of least resistance:
it's not just for electricity any more.
--------

Jason Grout

unread,
Aug 27, 2010, 7:30:15 AM8/27/10
to sage-r...@googlegroups.com
On 8/26/10 9:16 PM, Rob Beezer wrote:
> On Aug 26, 2:28 pm, Anthony David<ajdavi...@gmail.com> wrote:
>> The workaround is sufficient at this stage. I have only just started using
>> KDE as an experiment.
>
> KDE likes to default to Konqueror to handle various browser tasks,
> especially when you are in some other KDE application.
>
> Though Sage is not part of KDE, the notebook startup seems to find
> Konqueror and then chokes on the automated login of the admin user
> (IIRC).


In fact, a little while ago Ryan Grout traced down at least one problem
in Sage starting up Konqueror to a bug in Konqueror. I can't find the
bug now, but I've forwarded this message on to Ryan; hopefully he'll
post here. I believe the bug he found was different (konqueror keep
tried to open an infinite number of windows, it seemed), though.

Ryan, could you post the bug link for the bug you found in konqueror?

Jason


ayr0

unread,
Aug 27, 2010, 4:10:01 PM8/27/10
to sage-release
Hi,

The bug I experienced was closed in KDE 4.5. It was a problem in the
KDE systemsettings.
(Link. https://bugs.kde.org/show_bug.cgi?id=240677)j

Sage uses a couple of different methods to decide what webbrowser to
launch. The method that triggered the bug above was xdg-open.

One way to change the default webbrowser is to use KDE systemsettings
(in "Default Applications->Webbrowser"). Just change the field to
'firefox' and all KDE apps will call firefox instead (or whatever you
choose to use as your browser). I believe the change will occur
system-wide because KDE configures xdg-open (if I remember correctly).

Mitesh Patel

unread,
Aug 27, 2010, 8:17:13 PM8/27/10
to sage-r...@googlegroups.com


All 20000 of these passed, so the problem may well be in sage-test or
sage-doctest.

I've opened

http://trac.sagemath.org/sage_trac/ticket/9827

Mitesh Patel

unread,
Aug 27, 2010, 9:00:42 PM8/27/10
to sage-r...@googlegroups.com

A possible way to test this is to add one or more of these flags (see
'./sage -R --help'):

--no-save Don't save it [i.e., the workspace]
--no-environ Don't read the site and user environment files
--no-site-file Don't read the site-wide Rprofile
--no-init-file Don't read the user R profile
--no-restore-data Don't restore previously saved objects
--no-restore-history Don't restore the R history file
--no-restore Don't restore anything
--vanilla Combine --no-save, --no-restore, --no-site-file,
--no-init-file and --no-environ

For example, './sage -R --vanilla'.

georg grafendorfer

unread,
Aug 30, 2010, 8:58:25 AM8/30/10
to sage-release
> >> library /usr/local64.sfs/app/R/R_local/library_FC13 with no packages
> >> *not* added to lib path
> >> Attaching package of SfS goodies..
> >> Error in library(sfsmisc, keep.source = TRUE) :
> >>   there is no package called 'sfsmisc'
> >> In addition: Warning messages:
> >> 1: In libPIns(biocLibrary, beforeLib = file.path(RrootDir,
> >> "library"),  :
> >>   /usr/local64.sfs/app/R/Bioconductor/library_2.5_FC13 is not an
> >> existing directory
> >> 2: In libPIns(nlib = file.path(RrootDir, paste("library",
> >> R.maj.ver(),  :
> >>   .libPaths() contains no entries matching /usr/local64.sfs/app/R/
> >> R_local/library$
>
> > Is is possible that Sage's R is reading a system-wide/personal R
> > configuration file with these paths?
>
> A possible way to test this is to add one or more of these flags (see
> './sage -R --help'):
>
>   --no-save             Don't save it [i.e., the workspace]
>   --no-environ          Don't read the site and user environment files
>   --no-site-file        Don't read the site-wide Rprofile
>   --no-init-file        Don't read the user R profile
>   --no-restore-data     Don't restore previously saved objects
>   --no-restore-history  Don't restore the R history file
>   --no-restore          Don't restore anything
>   --vanilla             Combine --no-save, --no-restore, --no-site-file,
>                         --no-init-file and --no-environ
>
> For example, './sage -R --vanilla'.


this works fine:

ggeorg@maschke% ./sage -R --vanilla

R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> installed.packages()
Package
LibPath
base "base" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
datasets "datasets" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
grDevices "grDevices" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
graphics "graphics" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
grid "grid" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
methods "methods" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
splines "splines" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
stats "stats" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
stats4 "stats4" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
tcltk "tcltk" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
tools "tools" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
utils "utils" "/scratch/sage-4.5.3.alpha2/local/lib/R//
library"
Version Priority Bundle Contains Depends
base "2.10.1" "base" NA NA NA
datasets "2.10.1" "base" NA NA NA
grDevices "2.10.1" "base" NA NA NA
graphics "2.10.1" "base" NA NA NA
grid "2.10.1" "base" NA NA NA
methods "2.10.1" "base" NA NA NA
splines "2.10.1" "base" NA NA NA
stats "2.10.1" "base" NA NA NA
stats4 "2.10.1" "base" NA NA "methods, graphics, stats"
tcltk "2.10.1" "base" NA NA NA
tools "2.10.1" "base" NA NA NA
utils "2.10.1" "base" NA NA NA
Imports LinkingTo Suggests Enhances OS_type
base NA NA NA NA NA
datasets NA NA NA NA NA
grDevices NA NA NA NA NA
graphics "grDevices" NA NA NA NA
grid "grDevices" NA "lattice" NA NA
methods "utils" NA NA NA NA
splines "graphics, stats" NA NA NA NA
stats NA NA NA NA NA
stats4 NA NA NA NA NA
tcltk NA NA NA NA NA
tools NA NA NA NA NA
utils NA NA NA NA NA
License Built
base "Part of R 2.10.1" "2.10.1"
datasets "Part of R 2.10.1" "2.10.1"
grDevices "Part of R 2.10.1" "2.10.1"
graphics "Part of R 2.10.1" "2.10.1"
grid "Part of R 2.10.1" "2.10.1"
methods "Part of R 2.10.1" "2.10.1"
splines "Part of R 2.10.1" "2.10.1"
stats "Part of R 2.10.1" "2.10.1"
stats4 "Part of R 2.10.1" "2.10.1"
tcltk "Part of R 2.10.1" "2.10.1"
tools "Part of R 2.10.1" "2.10.1"
utils "Part of R 2.10.1" "2.10.1"
>

Georg

Mitesh Patel

unread,
Aug 30, 2010, 6:46:37 PM8/30/10
to sage-r...@googlegroups.com
> [...]

> Imports LinkingTo Suggests Enhances OS_type
> base NA NA NA NA NA
> datasets NA NA NA NA NA
> grDevices NA NA NA NA NA
> graphics "grDevices" NA NA NA NA
> grid "grDevices" NA "lattice" NA NA
> methods "utils" NA NA NA NA
> splines "graphics, stats" NA NA NA NA
> stats NA NA NA NA NA
> stats4 NA NA NA NA NA
> tcltk NA NA NA NA NA
> tools NA NA NA NA NA
> utils NA NA NA NA NA


It seems that just 12 of the expected 27 R packages have been built.
Could you give a link to the R build log

SAGE_ROOT/spkg/logs/r-2.10.1.p3.log

?

georg grafendorfer

unread,
Aug 31, 2010, 9:19:27 AM8/31/10
to sage-release

kcrisman

unread,
Aug 31, 2010, 9:50:27 AM8/31/10
to sage-release
Looks like none of the recommended packages installed, only the base
packages.

make[4]: Entering directory `/scratch/sage-4.5.3.alpha2/spkg/build/
r-2.10.1.p3/src/src/library/Recommended'
begin installing recommended package boot
Error in library(sfsmisc, keep.source = TRUE) :
there is no package called 'sfsmisc'
Calls: local ... eval.parent -> eval -> eval -> eval -> eval ->
library
In addition: Warning messages:
1: In libPIns(biocLibrary, beforeLib = file.path(RrootDir,
"library"), :
/usr/local64.sfs/app/R/Bioconductor/library_2.5_FC13 is not an
existing directory
2: In libPIns(nlib = file.path(RrootDir, paste("library",
R.maj.ver(), :
.libPaths() contains no entries matching ‘/usr/local64.sfs/app/R/
R_local/library$’
Execution halted
make[4]: *** [boot.ts] Error 1
make[4]: Leaving directory `/scratch/sage-4.5.3.alpha2/spkg/build/
r-2.10.1.p3/src/src/library/Recommended'
make[3]: *** [recommended-packages] Error 2
make[3]: Leaving directory `/scratch/sage-4.5.3.alpha2/spkg/build/
r-2.10.1.p3/src/src/library/Recommended'
make[2]: *** [stamp-recommended] Error 2
make[2]: Leaving directory `/scratch/sage-4.5.3.alpha2/spkg/build/
r-2.10.1.p3/src'
make[2]: Entering directory `/scratch/sage-4.5.3.alpha2/spkg/build/
r-2.10.1.p3/src'
mkdir -p -- /scratch/sage-4.5.3.alpha2/local/lib/R

This seems related to

> > >>>> Attaching package of SfS goodies..
> > >>>> Error in library(sfsmisc, keep.source = TRUE) :
> > >>>>   there is no package called 'sfsmisc'

in the original report. This is *not* a recommended package. It
*does* live at ETHZ, though! Georg, is it possible that there is some
global thing that tries to install this in any R at www.math.ethz.ch
once the base packages have been put in, but since it's not part of
'our' Sage R it exits instead?

- kcrisman

georg grafendorfer

unread,
Aug 31, 2010, 3:32:19 PM8/31/10
to sage-release
There is an environment variable R_PROFILE (see explanation here:
http://biom1.univ-lyon1.fr/library/base/html/Startup.html ), which
points to the following file

http://www.math.ethz.ch/~ggeorg/Rprofile

So I tried

ggeorg@maschke% export R_PROFILE=
ggeorg@maschke% echo $R_PROFILE

ggeorg@maschke% make ptestlong

but got the same doctest failure,
do I have to rebuild sage in such an environment?

Georg

kcrisman

unread,
Aug 31, 2010, 4:03:45 PM8/31/10
to sage-release


On Aug 31, 3:32 pm, georg grafendorfer <georg.grafendor...@gmail.com>
wrote:
> There is an environment variable R_PROFILE (see explanation here:http://biom1.univ-lyon1.fr/library/base/html/Startup.html), which
> points to the following file
>
> http://www.math.ethz.ch/~ggeorg/Rprofile
>
> So I tried
>
> ggeorg@maschke% export R_PROFILE=
> ggeorg@maschke% echo $R_PROFILE
>
> ggeorg@maschke% make ptestlong
>
> but got the same doctest failure,
> do I have to rebuild sage in such an environment?

make ptestlong probably only does the testing, since Sage is already
built. But you shouldn't have to rebuild all of Sage.

./sage -f r

should "f"orce reinstall the "r" package (you would do r-x.y.z for a
specific version of the package, but this would do the "right" one)
for you, and let's keep our fingers crossed that this would work.

In particular, it looks like

MSG("Attaching package of SfS goodies.. ")
## want to see comments:
require(stats, quietly = TRUE)
library(sfsmisc, keep.source = TRUE)

is always being called right in the middle of the build process. I
have to admit I couldn't follow the many {} pairs to find out when it
is called :) But let's hope this is the issue.

- kcrisman

Georg Grafendorfer

unread,
Sep 1, 2010, 5:25:38 AM9/1/10
to sage-release
OK, I did

$ export R_PROFILE=
$ ./sage -f r
$ make ptestlong

all doctest passed, no failures

Georg

Mitesh Patel

unread,
Sep 1, 2010, 5:55:34 AM9/1/10
to sage-r...@googlegroups.com
On 09/01/2010 04:25 AM, Georg Grafendorfer wrote:
> On Aug 31, 10:03 pm, kcrisman <kcris...@gmail.com> wrote:
>> On Aug 31, 3:32 pm, georg grafendorfer <georg.grafendor...@gmail.com>
>> wrote:
>>> On Aug 31, 3:50 pm, kcrisman <kcris...@gmail.com> wrote:
>>>> Looks like none of the recommended packages installed, only the base
>>>> packages.
>>>> [...]


I've opened

http://trac.sagemath.org/sage_trac/ticket/9847

for the R_PROFILE problem and

http://trac.sagemath.org/sage_trac/ticket/9848

for mentioning the '-R' flag in the 'sage -advanced' help message.

kcrisman

unread,
Sep 1, 2010, 8:55:04 AM9/1/10
to sage-release


On Sep 1, 5:25 am, Georg Grafendorfer <georg.grafendor...@gmail.com>
Great!
Reply all
Reply to author
Forward
0 new messages