From ripley at stats.ox.ac.uk  Wed Nov 14 00:06:43 2007
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Tue, 13 Nov 2007 23:06:43 +0000 (GMT)
Subject: [Rd] R 2.6.0 make check fails on SGI origin 350 and
In-Reply-To: <64596DC1-C0A3-4671-B7AE-CEB5EA5DFADE@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>
Message-ID: <Pine.LNX.4.64.0711132259350.19784@gannet.stats.ox.ac.uk>

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



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