From ripley at stats.ox.ac.uk  Wed Nov 14 08:09:16 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 14 Nov 2007 07:09:16 +0000 (GMT)
Subject: [Rd] R 2.6.0 make check fails on SGI origin 350 and
In-Reply-To: <A22187A3-26C9-4F02-8016-131353D6F0C9@ualberta.ca>
References: <42665B36-6FE2-48A4-A1C4-09F67D61A28C@ualberta.ca>
	<Pine.LNX.4.64.0711062341250.30885@gannet.stats.ox.ac.uk>
	<A8521DA1-CFA8-4B2D-896B-690AF301E122@ualberta.ca>
	<18226.54375.972183.286953@stat.math.ethz.ch>
	<6B3A01D9-B6A9-483A-9EA6-013BA8743BDD@ualberta.ca>
	<18227.19165.686297.222253@stat.math.ethz.ch>
	<39B05A63-0B09-4C15-983C-4FCC51641A0B@ualberta.ca>
	<64596DC1-C0A3-4671-B7AE-CEB5EA5DFADE@ualberta.ca>
	<Pine.LNX.4.64.0711132259350.19784@gannet.stats.ox.ac.uk>
	<A22187A3-26C9-4F02-8016-131353D6F0C9@ualberta.ca>
Message-ID: <Pine.LNX.4.64.0711140701390.5265@gannet.stats.ox.ac.uk>

On Tue, 13 Nov 2007, kamil Marcinkowski wrote:

> Hello List, Prof Brian Ripley
>
> How would the inefficiencies in IEC60559 arithmetic handling affect a user,
> Slow computations or compromised data and calculations?

Just a loss of accuracy.  There have been systems in which using extreme 
values causes a large loss of speed, but you are unlikely to encounter 
one.

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

This shows a bug in the systems' strptime.  This looks like the bug 
mentioned (with a fix) in the R-admin manual under IRIX.


>
>> 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
>
>
> "This communication is intended for the use of the recipient to which it is
> addressed, and may contain confidential, personal, and/or privileged
> information.  Please contact us immediately if you are not the intended
> recipient of this communication.  If you are not the intended recipient of
> this communication, do not copy, distribute, or take action on it. Any
> communication received in error, or subsequent reply, should be deleted or
> destroyed."
>
>
>
> 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 at 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
>> 
>

-- 
Brian D. Ripley,                  ripley at 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



[Rd] R 2.6.0 make check fails on SGI origin 350 and
Prof Brian Ripley