Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and

From: kamil Marcinkowski <kamil_at_ualberta.ca>
Date: Tue, 13 Nov 2007 17:04:16 -0700

Hello List, Prof Brian Ripley

How would the inefficiencies in IEC60559 arithmetic handling affect a user,
Slow computations or compromised data and calculations?

Here are the last 50 lines of the reg-tests-1.Rout.fail file.

> root_at_nexus:70# tail -50 reg-tests-1.Rout.fail
> > ## first two gave error in 1.8.1
> >
> >
> > ## PR#4558 part 2
> > x <- seq(as.POSIXct("2004-03-25"), as.POSIXct("2004-03-31"),
> by="DSTdays")
> > stopifnot(length(x) == 7)
> > ## was length 6 in the UK time zone.
> >
> >
> > ## PR#6702 c/rbind on list matrices
> > A <- matrix(as.list(1:4), 2, 2)
> > (res <- cbind(A, A))
> [,1] [,2] [,3] [,4]
> [1,] 1 3 1 3
> [2,] 2 4 2 4
> > stopifnot(typeof(res) == "list")
> > (res <- rbind(A, A))
> [,1] [,2]
> [1,] 1 3
> [2,] 2 4

> [3,] 1 3

> [4,] 2 4
> > stopifnot(typeof(res) == "list")
> > ## were not implemented in 1.8.1
> >
> >
> > ## Date objects with NA's
> > (t1 <- strptime(c("6. Aug. 1930", "3. Nov. 1925", "28. Mar. 1959",
> + NA, paste(1:29," Feb. 1960", sep=".")),
> + format = "%d. %b. %Y"))
> [1] "1930-08-06 MST7MDT" "1925-11-03 MST7MDT" "1959-03-28 MST7MDT"
> [4] NA "1960-02-01 MST7MDT" "1960-02-02 MST7MDT"
> [7] "1960-02-03 MST7MDT" "1960-02-04 MST7MDT" "1960-02-05 MST7MDT"
> [10] "1960-02-06 MST7MDT" "1960-02-07 MST7MDT" "1960-02-08 MST7MDT"
> [13] "1960-02-09 MST7MDT" "1960-02-10 MST7MDT" "1960-02-11 MST7MDT"
> [16] "1960-02-12 MST7MDT" "1960-02-13 MST7MDT" "1960-02-14 MST7MDT"
> [19] "1960-02-15 MST7MDT" "1960-02-16 MST7MDT" "1960-02-17 MST7MDT"
> [22] "1960-02-18 MST7MDT" "1960-02-19 MST7MDT" "1960-02-20 MST7MDT"
> [25] "1960-02-21 MST7MDT" "1960-02-22 MST7MDT" "1960-02-23 MST7MDT"
> [28] "1960-02-24 MST7MDT" "1960-02-25 MST7MDT" "1960-02-26 MST7MDT"
> [31] "1960-02-27 MST7MDT" "1960-02-28 MST7MDT" "1960-02-29 MST7MDT"
> > stopifnot(6 == length(print(s1 <- summary(t1))),
> + s1== summary(as.POSIXct(t1)),
> + 6 == length(print(format(as.Date(s1)))) )
> Min. 1st Qu. Median Mean 3rd Qu. Max.
> NA NA NA NA NA NA
> Min. 1st Qu. Median Mean 3rd Qu. Max.
> NA NA NA NA NA NA
> Error: s1 == summary(as.POSIXct(t1)) is not all TRUE
> Execution halted

>

Cheers,

Kamil

Kamil Marcinkowski                   Westgrid System Administrator
kamil_at_ualberta.ca                     University of Alberta site
  Tel.780 492-0354                     Research Computing Support
Fax.780 492-1729                     Academic ICT
Edmonton, Alberta, CANADA University of Alberta

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On 13-Nov-07, at 4:06 PM, Prof Brian Ripley wrote:

> The perl-related warnings have gone in R-devel: we now take the view
> that since we need perl to make the test suite, perl >= 5.8.0 is
> compulsory. (5.6.1 is now over 7 years' old, and 5.8.0 is more than
> 5.)

>

> The make check failure is in reg-tests-1.R and so will show up in
> reg-tests-1.Rout.fail. What is at the bottom of that file?
>

> The rest seem to indicate infelicities in how IEC60559 arithmetic is
> handled, e.g the particular NaN that represents NA not being
> propagated correctly and non-use of denormalized numbers.
>

> On Tue, 13 Nov 2007, kamil Marcinkowski wrote:
>
>> Hello list
>>
>> Thank you for your help with the d-p-q-r-tests on Irix.
>>
>> After patching d-p-q-r-tests.R, and d-p-q-r-tests.Rout.save file to
>> reflect the
>> change, d-p-q-r tests succeed but  make check still fails:
>>
>>> comparing 'complex.Rout' to './complex.Rout.save' ...188c188
>>> < [1] 0+0i
>>> ---
>>>> [1] 1.6789e-308+0i
>>> OK
>>> running code in 'print-tests.R' ... OK
>>> comparing 'print-tests.Rout' to './print-tests.Rout.save' ...256c256
>>> < [1] 9
>>> ---
>>>> [1] 11
>>> 260c260
>>> < [1]  0.000000e+00 2.225074e-308 2.225074e-308 2.227299e-308
>>> 2.447581e-308
>>> ---
>>>> [1] 2.002566e-308 2.222849e-308 2.225074e-308 2.225074e-308
>>> 2.225074e-308 2.227299e-308 2.447581e-308
>>> 266c266
>>> < [1]  0.000000e+00  0.000000e+00  0.000000e+00 2.447581e-308
>>> 1.566452e-306 1.253162e-305
>>> ---
>>>> [1] 2.002566e-308 2.447581e-308 1.281643e-306 1.566452e-306
>>> 1.025314e-305 1.253162e-305
>>> 269,273c269,273
>>> < [1,]  0e+00  0e+00  0.0e+00  0.00e+00  0.000e+00  0.0000e+00
>>> 0.00000e+00
>>> < [2,]  0e+00  0e+00  0.0e+00  0.00e+00  0.000e+00  0.0000e+00
>>> 0.00000e+00
>>> < [3,]  0e+00  0e+00  0.0e+00  0.00e+00  0.000e+00  0.0000e+00
>>> 0.00000e+00
>>> < [4,]  0e+00  0e+00 2.4e-308 2.45e-308 2.448e-308 2.4476e-308
>>> 2.44758e-308
>>> < [5,] 2e-306 2e-306 1.6e-306 1.57e-306 1.566e-306 1.5665e-306
>>> 1.56645e-306
>>> ---
>>>> [1,] 2e-308 2e-308 2.0e-308 2.00e-308 2.003e-308 2.0026e-308
>>> 2.00257e-308
>>>> [2,] 2e-308 2e-308 2.4e-308 2.45e-308 2.448e-308 2.4476e-308
>>> 2.44758e-308
>>>> [3,] 1e-306 1e-306 1.3e-306 1.28e-306 1.282e-306 1.2816e-306
>>> 1.28164e-306
>>>> [4,] 2e-306 2e-306 1.6e-306 1.57e-306 1.566e-306 1.5665e-306
>>> 1.56645e-306
>>>> [5,] 1e-305 1e-305 1.0e-305 1.03e-305 1.025e-305 1.0253e-305
>>> 1.02531e-305
>>> 355c355
>>> < 4.141593+  1i 4.341593+ 10i      NaN+NaNi      Inf+  0i     -Inf
>>> +NaNi      NaN+Infi
>>> ---
>>>> 4.141593+  1i 4.341593+ 10i            NA      Inf+  0i     -Inf
>>> +NaNi      NaN+Infi
>>> 358c358
>>> < [1,] 4.141593+ 1i NaN+NaNi -Inf+NaNi
>>> ---
>>>> [1,] 4.141593+ 1i     NA -Inf+NaNi
>>> 364c364
>>> < [3,] NaN+      NaNi  NaN+     Infi
>>> ---
>>>> [3,]             NA  NaN+     Infi
>>> OK
>>> running code in 'datasets.R' ... OK
>>> comparing 'datasets.Rout' to './datasets.Rout.save' ... OK
>>> running code in 'lapack.R' ... OK
>>> comparing 'lapack.Rout' to './lapack.Rout.save' ... OK
>>> gmake[3]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/tests'
>>> gmake[2]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/tests'
>>> gmake[2]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/tests'
>>> running regression tests
>>> gmake[3]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/tests'
>>> running code in 'reg-tests-1.R' ...gmake[3]: *** [reg-tests-1.Rout]
>>> Error 1
>>> gmake[3]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/tests'
>>> gmake[2]: *** [test-Reg] Error 2
>>> gmake[2]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/tests'
>>> gmake[1]: *** [test-all-basics] Error 1
>>> gmake[1]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/tests'
>>> gmake: *** [check] Error 2
>>>
>>
>>
>> Also since we are using perl 5.6 on the system; the documentation
>> system did not build.
>>
>>> root_at_nexus:104#	perl -v
>>> This is perl, v5.6.1 built for irix-n32
>>
>>
>> configure output:
>>> checking for perl... /usr/sbin/perl
>>> checking whether perl version is at least 5.8.0... Perl v5.8.0
>>> required--this is only v5.6.1, stopped at -e line 1.
>>> no
>>> configure: WARNING: you cannot build the object documentation system
>>
>>
>> The following errors occurred during gmake check:
>>
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/base/R-ex cannot be opened at ../../share/perl/
>>> massage-Examples.pl line 129.
>>> running code in 'base-Ex.R' ... OK
>>> collecting examples for package 'tools' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/tools/R-ex cannot be opened at ../../share/perl/
>>> massage-Examples.pl line 129.
>>> running code in 'tools-Ex.R' ... OK
>>> collecting examples for package 'utils' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/utils/R-ex cannot be opened at ../../share/perl/
>>> massage-Examples.pl line 129.
>>> running code in 'utils-Ex.R' ... OK
>>> collecting examples for package 'grDevices' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/grDevices/R-ex cannot be opened at ../../share/
>>> perl/massage-Examples.pl line 129.
>>> running code in 'grDevices-Ex.R' ... OK
>>> collecting examples for package 'graphics' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/graphics/R-ex cannot be opened at ../../share/
>>> perl/massage-Examples.pl line 129.
>>> running code in 'graphics-Ex.R' ... OK
>>> collecting examples for package 'stats' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/stats/R-ex cannot be opened at ../../share/perl/
>>> massage-Examples.pl line 129.
>>> running code in 'stats-Ex.R' ... OK
>>> collecting examples for package 'datasets' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/datasets/R-ex cannot be opened at ../../share/
>>> perl/massage-Examples.pl line 129.
>>> running code in 'datasets-Ex.R' ... OK
>>> collecting examples for package 'methods' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/methods/R-ex cannot be opened at ../../share/ 
>>> perl/
>>> massage-Examples.pl line 129.
>>> running code in 'methods-Ex.R' ... OK
>>> collecting examples for package 'grid' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/grid/R-ex cannot be opened at ../../share/perl/
>>> massage-Examples.pl line 129.
>>> running code in 'grid-Ex.R' ... OK
>>> collecting examples for package 'splines' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/splines/R-ex cannot be opened at ../../share/ 
>>> perl/
>>> massage-Examples.pl line 129.
>>> running code in 'splines-Ex.R' ... OK
>>> collecting examples for package 'stats4' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>> gmake[5]: Leaving directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> file ../../library/stats4/R-ex cannot be opened at ../../share/perl/
>>> massage-Examples.pl line 129.
>>> running code in 'stats4-Ex.R' ... OK
>>> collecting examples for package 'tcltk' ...
>>> gmake[5]: Entering directory `/usr/global/R-build/R-2.6.0-
>>> patched-11-08-07/src/library'
>>> you need Perl version 5 to build the R object docs
>>> gmake[5]: *** [Rdfiles] Error 1
>>
>>
>> I figure these errors are just the inability to create documentation,
>> but mention them in case they may be relevant or important.
>>
>> Thanks,
>>
>> Kamil
>>
>> Kamil Marcinkowski                   Westgrid System Administrator
>> kamil_at_ualberta.ca                     University of Alberta site
>> Tel.780 492-0354                     Research Computing Support
>> Fax.780 492-1729                     Academic ICT
>> Edmonton, Alberta, CANADA    University of Alberta
>>
>>
>> "This communication is intended for the use of the recip... 
>> {{dropped:18}}
>>
>> ______________________________________________
>> R-devel_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>

> --
> Brian D. Ripley, ripley@stats.ox.ac.uk
> Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
> University of Oxford, Tel: +44 1865 272861 (self)
> 1 South Parks Road, +44 1865 272866 (PA)
> Oxford OX1 3TG, UK Fax: +44 1865 272595
> [[alternative HTML version deleted]] ______________________________________________ R-devel_at_r-project.org mailing list

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