Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
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.
>
>> [EMAIL PROTECTED]: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,] 1313
>> [2,] 2424
>>> stopifnot(typeof(res) == "list")
>>> (res <- rbind(A, A))
>> [,1] [,2]
>> [1,] 13
>> [2,] 24
>> [3,] 13
>> [4,] 24
>>> 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. MedianMean 3rd Qu.Max.
>> NA NA NA NA NA NA
>> Min. 1st Qu. MedianMean 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
> [EMAIL PROTECTED] University of Alberta site
> Tel.780 492-0354 Research Computing Support
> Fax.780 492-1729 Academic ICT
> Edmonton, Alberta, CANADAUniversity 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] 0.00e+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] 0.00e+00 0.00e+00 0.00e+00 2.447581e-308
1.566452e-306 1.253162e-
Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
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.
> [EMAIL PROTECTED]: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,] 1313
> [2,] 2424
> > stopifnot(typeof(res) == "list")
> > (res <- rbind(A, A))
> [,1] [,2]
> [1,] 13
> [2,] 24
> [3,] 13
> [4,] 24
> > 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. MedianMean 3rd Qu.Max.
> NA NA NA NA NA NA
>Min. 1st Qu. MedianMean 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
[EMAIL PROTECTED] University of Alberta site
Tel.780 492-0354 Research Computing Support
Fax.780 492-1729 Academic ICT
Edmonton, Alberta, CANADAUniversity 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] 0.00e+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] 0.00e+00 0.00e+00 0.00e+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.e+00
>>> 0.0e+00
>>> < [2,] 0e+00 0e+00 0.0e+00 0.00e+00 0.000e+00 0.e+00
>>> 0.0e+00
>>> < [3,] 0e+00 0e+00 0.0e+00 0.00e+00 0.000e+00 0.e+00
>>> 0.0e+00
>>> < [4,] 0e+00 0e+00 2.4e-308 2.45e-308 2.448e-308
Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
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] 0.00e+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] 0.00e+00 0.00e+00 0.00e+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.e+00 >> 0.0e+00 >> < [2,] 0e+00 0e+00 0.0e+00 0.00e+00 0.000e+00 0.e+00 >> 0.0e+00 >> < [3,] 0e+00 0e+00 0.0e+00 0.00e+00 0.000e+00 0.e+00 >> 0.0e+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+ 10iNA 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. > >> [EMAIL PROTECTED]: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'
Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
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] 0.00e+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] 0.00e+00 0.00e+00 0.00e+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.e+00 > 0.0e+00 > < [2,] 0e+00 0e+00 0.0e+00 0.00e+00 0.000e+00 0.e+00 > 0.0e+00 > < [3,] 0e+00 0e+00 0.0e+00 0.00e+00 0.000e+00 0.e+00 > 0.0e+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+ 10iNA 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. > [EMAIL PROTECTED]: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 'grDevice
Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
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] 0.00e+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] 0.00e+00 0.00e+00 0.00e+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.e+00 > 0.0e+00 > < [2,] 0e+00 0e+00 0.0e+00 0.00e+00 0.000e+00 0.e+00 > 0.0e+00 > < [3,] 0e+00 0e+00 0.0e+00 0.00e+00 0.000e+00 0.e+00 > 0.0e+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+ 10iNA 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. > [EMAIL PROTECTED]: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 'grDevice
Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
Thanks a lot Kamil,
for the confirmation:
> "kM" == kamil Marcinkowski <[EMAIL PROTECTED]>
> on Thu, 8 Nov 2007 09:41:05 -0700 writes:
kM> Hello list
kM> Here are the results of the tests on R 2.6.0 patched:
>> R version 2.6.0 Patched (2007-11-05 r43362)
>> Copyright (C) 2007 The R Foundation for Statistical Computing
>> ISBN 3-900051-07-0
kM> ...
>> > str(.Machine, digits=7)
>> List of 18
>> $ double.eps : num 2.220446e-16
>> $ double.neg.eps : num 1.110223e-16
>> $ double.xmin : num 2.225074e-308
>> $ double.xmax : num 1.797693e+308
>> $ double.base : int 2
>> $ double.digits: int 53
>> $ double.rounding : int 2
>> $ double.guard : int 0
>> $ double.ulp.digits: int -52
>> $ double.neg.ulp.digits: int -53
>> $ double.exponent : int 11
>> $ double.min.exp : int -1022
>> $ double.max.exp : int 1024
>> $ integer.max : int 2147483647
>> $ sizeof.long : int 4
>> $ sizeof.longlong : int 8
>> $ sizeof.longdouble: int 16
>> $ sizeof.pointer : int 4
>>
>> > dpois( 10, 10^(-290:-310), log=TRUE)
>> [1] -6692.601 -6715.627 -6738.653 -6761.679 -6784.705 -6807.730 -6830.756
>> [8] -6853.782 -6876.808 -6899.834 -6922.860 -6945.886 -6968.911 -6991.937
>> [15] -7014.963 -7037.989 -7061.015 -7084.041 -Inf -Inf -Inf
>>
>> > All.eq(dpois( 10*1:2, 3e-308, log=TRUE), c(-7096.08037610806,
>> -14204.2875435307))
>> Error: could not find function "All.eq"
kM> I copied the All.eq function from d-p-q-r-tests.R file and rerun he
kM> test:
>> > All.eq <- function(x,y) {
>> all.equal.numeric(x,y, tolerance= 64*.Machine$double.eps,
>> scale = max(0, mean(abs(x), na.rm=TRUE)))
>> }
>> + + + >
>> > All.eq(dpois( 10*1:2, 3e-308, log=TRUE), c(-7096.08037610806,
>> -14204.2875435307))
>> [1] TRUE
Very good.
So after, the SGI only has slight problems with so-called
denormalized numbers; this is not considered a big problem
and the next versions of R will have the check above, instead of
the one that gave an error.
Thank you again for your feedback!
Regards,
Martin Maechler, ETH Zurich
kM> Cheers,
kM> Kamil
kM> Kamil Marcinkowski Westgrid System Administrator
kM> [EMAIL PROTECTED] University of Alberta site
kM> Tel.780 492-0354 Research Computing Support
kM> Fax.780 492-1729 Academic ICT
kM> Edmonton, Alberta, CANADAUniversity of Alberta
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Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
Hello list
Here are the results of the tests on R 2.6.0 patched:
> R version 2.6.0 Patched (2007-11-05 r43362)
> Copyright (C) 2007 The R Foundation for Statistical Computing
> ISBN 3-900051-07-0
...
> > str(.Machine, digits=7)
> List of 18
> $ double.eps : num 2.220446e-16
> $ double.neg.eps : num 1.110223e-16
> $ double.xmin : num 2.225074e-308
> $ double.xmax : num 1.797693e+308
> $ double.base : int 2
> $ double.digits: int 53
> $ double.rounding : int 2
> $ double.guard : int 0
> $ double.ulp.digits: int -52
> $ double.neg.ulp.digits: int -53
> $ double.exponent : int 11
> $ double.min.exp : int -1022
> $ double.max.exp : int 1024
> $ integer.max : int 2147483647
> $ sizeof.long : int 4
> $ sizeof.longlong : int 8
> $ sizeof.longdouble: int 16
> $ sizeof.pointer : int 4
>
> > dpois( 10, 10^(-290:-310), log=TRUE)
> [1] -6692.601 -6715.627 -6738.653 -6761.679 -6784.705 -6807.730
> -6830.756
> [8] -6853.782 -6876.808 -6899.834 -6922.860 -6945.886 -6968.911
> -6991.937
> [15] -7014.963 -7037.989 -7061.015 -7084.041 -Inf -
> Inf -Inf
>
> > All.eq(dpois( 10*1:2, 3e-308, log=TRUE), c(-7096.08037610806,
> -14204.2875435307))
> Error: could not find function "All.eq"
I copied the All.eq function from d-p-q-r-tests.R file and rerun he
test:
> > All.eq <- function(x,y) {
> all.equal.numeric(x,y, tolerance= 64*.Machine$double.eps,
> scale = max(0, mean(abs(x), na.rm=TRUE)))
> }
> + + + >
> > All.eq(dpois( 10*1:2, 3e-308, log=TRUE), c(-7096.08037610806,
> -14204.2875435307))
> [1] TRUE
>
Cheers,
Kamil
Kamil Marcinkowski Westgrid System Administrator
[EMAIL PROTECTED] University of Alberta site
Tel.780 492-0354 Research Computing Support
Fax.780 492-1729 Academic ICT
Edmonton, Alberta, CANADAUniversity 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
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>
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Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
> "kM" == kamil Marcinkowski <[EMAIL PROTECTED]> > on Tue, 6 Nov 2007 17:02:56 -0700 writes: kM> Hello Prof Brian Ripley and list kM> There is no "d-p-q-r-tests.Rout" file, the following files do exists kM> and are being sent as attachments: kM> ./tests/d-p-q-r-tests.R , kM> ./tests/d-p-q-r-tests.Rout.save , kM> ./tests/d-p-q-r-tests.Rout.fail . Thank you , Kamil. It's only the fail one that is interesting to us (the other two are part of the R sources!). However, for attachments to make it through the anti-virus anti-spam filters, you need to give them MIME-type 'text/*' typically 'text/plain' whereas many e-mail programs nowadays just blindly put 'application/octet-stream' ... the same format that viruses are often using as well. One way to help your e-mail software to use the proper mime type, may be to rename the file to something like d-p-q-r-tests_Rout_fail.txt With regards, Martin Maechler, ETH Zurich __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
Hello Prof Brian Ripley and list There is no "d-p-q-r-tests.Rout" file, the following files do exists and are being sent as attachments: ./tests/d-p-q-r-tests.R , ./tests/d-p-q-r-tests.Rout.save , ./tests/d- p-q-r-tests.Rout.fail . Cheers, Kamil Kamil Marcinkowski Westgrid System Administrator [EMAIL PROTECTED] University of Alberta site Tel.780 492-0354 Research Computing Support Fax.780 492-1729 Academic ICT Edmonton, Alberta, CANADAUniversity 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 6-Nov-07, at 4:46 PM, Prof Brian Ripley wrote: > We need to see the d-p-q-r-tests.Rout file, and perhaps ask for some > more runs (unfortunately that line number is after massaging). Can > you make it available to us? Or at least a portion containing the > quoted line (which should only occur once)? > > On Tue, 6 Nov 2007, kamil Marcinkowski wrote: > >> Hello >> >> I am trying to install R 2.6.0 on a SGI Origin 350 running IRIX 6.5 >> 6.5.28f >> >> R was configured with the following options: >> >>> --x-includes=/usr/include/X11 >>> --x-libraries=/usr/lib/X11 >>> --includedir=/usr/freeware/include >>> --includedir=/usr/freeware/lib32 >>> --includedir=/usr/freeware/lib64 >>> --with-readline=no >>> --with-iconv=no >>> CC=cc >> >> >> gmake complied successfully, however gmake check failed on d-p-q-r- >> tests.R . >> >>> running code in 'd-p-q-r-tests.R' ... OK >>> comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... >>> 959c959 >>> < [1] "Mean scaled difference: NaN" >>> --- [1] TRUE >>> gmake[3]: *** [d-p-q-r-tests.Rout] Error 1 >>> gmake[3]: Leaving directory `/usr/global/R-build/R-2.6.0/tests' >>> gmake[2]: *** [test-Specific] Error 2 >>> gmake[2]: Leaving directory `/usr/global/R-build/R-2.6.0/tests' >>> gmake[1]: *** [test-all-basics] Error 1 >>> gmake[1]: Leaving directory `/usr/global/R-build/R-2.6.0/tests' >>> gmake: *** [check] Error 2 >> >> >> Any ideas would be appreciated. >> >> Cheers, >> >> Kamil >> >> Kamil Marcinkowski Westgrid System Administrator >> [EMAIL PROTECTED] University of Alberta site >> Tel.780 492-0354 Research Computing Support >> Fax.780 492-1729 Academic ICT >> Edmonton, Alberta, CANADAUniversity 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." >> >> >> >> >> [[alternative HTML version deleted]] >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > -- > Brian D. Ripley, [EMAIL PROTECTED] > 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, UKFax: +44 1865 272595 > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.6.0 make check fails on SGI origin 350 and
We need to see the d-p-q-r-tests.Rout file, and perhaps ask for some more runs (unfortunately that line number is after massaging). Can you make it available to us? Or at least a portion containing the quoted line (which should only occur once)? On Tue, 6 Nov 2007, kamil Marcinkowski wrote: > Hello > > I am trying to install R 2.6.0 on a SGI Origin 350 running IRIX 6.5 > 6.5.28f > > R was configured with the following options: > >> --x-includes=/usr/include/X11 >> --x-libraries=/usr/lib/X11 >> --includedir=/usr/freeware/include >> --includedir=/usr/freeware/lib32 >> --includedir=/usr/freeware/lib64 >> --with-readline=no >> --with-iconv=no >> CC=cc > > > gmake complied successfully, however gmake check failed on d-p-q-r- > tests.R . > >> running code in 'd-p-q-r-tests.R' ... OK >> comparing 'd-p-q-r-tests.Rout' to './d-p-q-r-tests.Rout.save' ... >> 959c959 >> < [1] "Mean scaled difference: NaN" >> --- >>> [1] TRUE >> gmake[3]: *** [d-p-q-r-tests.Rout] Error 1 >> gmake[3]: Leaving directory `/usr/global/R-build/R-2.6.0/tests' >> gmake[2]: *** [test-Specific] Error 2 >> gmake[2]: Leaving directory `/usr/global/R-build/R-2.6.0/tests' >> gmake[1]: *** [test-all-basics] Error 1 >> gmake[1]: Leaving directory `/usr/global/R-build/R-2.6.0/tests' >> gmake: *** [check] Error 2 > > > Any ideas would be appreciated. > > Cheers, > > Kamil > > Kamil Marcinkowski Westgrid System Administrator > [EMAIL PROTECTED] University of Alberta site > Tel.780 492-0354 Research Computing Support > Fax.780 492-1729 Academic ICT > Edmonton, Alberta, CANADAUniversity 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." > > > > > [[alternative HTML version deleted]] > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- Brian D. Ripley, [EMAIL PROTECTED] 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, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
