Berend,
I have compiled gmp on an older machine (2008 MacPro) - in fact the same that
we used until 4.0.0. Apparently there are some new instruction on more recent
CPUs that gmp leverages if it finds them. Oddly, I could not find any good info
on this so it's hard to pin-point the difference or exact CPUs that cause this.
Using the old one should make it fairly safe.
Cheers,
Simon
> On 17/04/2020, at 1:38 AM, Berend Hasselman <b...@xs4all.nl> wrote:
>
> Simon,
>
> The issue has gone away. Hurrah!
>
> But what actually was the problem and how did you solve it?
>
> regards and many thanks,
>
> Berend
>
>
>> On 16 Apr 2020, at 15:26, Simon Urbanek <simon.urba...@r-project.org> wrote:
>>
>> Thanks, please re-install Rmpfr and gmp from the Mac master mirror:
>>
>> install.packages(c("gmp","Rmpfr"),repos="https://mac.R-project.org";)
>>
>> and let me know if the issue goes away.
>>
>> Thanks,
>> Simon
>>
>>
>>
>>
>>> On 16/04/2020, at 7:21 PM, carsten.dorm...@biom.uni-freiburg.de wrote:
>>>
>>> Can confirm problem:
>>>
>>>> dpois(mpfr(x, 120), 1000)
>>>
>>> *** caught illegal operation ***
>>> address 0x1116f7c42, cause 'illegal opcode'
>>>
>>> Traceback:
>>> 1: .class1(object)
>>> 2: as(value, dataClass)
>>> 3: setDataPart(x, .Call(Math_mpfr, x, .Math.codes[[.Generic]]))
>>> 4: exp(-lambda)
>>> 5: exp(-lambda)
>>> 6: dpois(mpfr(x, 120), 1000)
>>>
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>> Selection:
>>>
>>>
>>>> sessionInfo() # after restart
>>> R version 4.0.0 alpha (2020-04-01 r78130)
>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>> Running under: macOS Mojave 10.14.6
>>>
>>> Matrix products: default
>>> BLAS:
>>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
>>> LAPACK:
>>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>>>
>>> locale:
>>> [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> loaded via a namespace (and not attached):
>>> [1] compiler_4.0.0
>>>
>>>
>>> Carsten
>>>
>>>
>>>> On 16. Apr 2020, at 08:56, Berend Hasselman <b...@xs4all.nl> wrote:
>>>>
>>>>
>>>> If the pre-release binary of Rmpfr is intended for the R-4.0 beta then I
>>>> am experiencing "illegal operations" with "illegal opcode" errors.
>>>>
>>>> <sessionInfo>
>>>>
>>>> R version 4.0.0 beta (2020-04-14 r78227)
>>>> Platform: x86_64-apple-darwin17.0 (64-bit)
>>>> Running under: macOS Catalina 10.15.4
>>>>
>>>> Matrix products: default
>>>> BLAS:
>>>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
>>>> LAPACK:
>>>> /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
>>>>
>>>> locale:
>>>> [1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8
>>>>
>>>> attached base packages:
>>>> [1] stats graphics grDevices utils datasets methods base
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] compiler_4.0.0
>>>>
>>>> </sessionInfo>
>>>>
>>>> A simple example session is
>>>>
>>>> <(in+output)>
>>>>
>>>>> library(gmp,lib.loc=".");library(Rmpfr,lib.loc=".")
>>>>
>>>> Attaching package: 'gmp'
>>>>
>>>> The following objects are masked from 'package:base':
>>>>
>>>> %*%, apply, crossprod, matrix, tcrossprod
>>>>
>>>> C code of R package 'Rmpfr': GMP using 64 bits per limb
>>>>
>>>>
>>>> Attaching package: 'Rmpfr'
>>>>
>>>> The following object is masked from 'package:gmp':
>>>>
>>>> outer
>>>>
>>>> The following objects are masked from 'package:stats':
>>>>
>>>> dbinom, dgamma, dnorm, dpois, pnorm
>>>>
>>>> The following objects are masked from 'package:base':
>>>>
>>>> cbind, pmax, pmin, rbind
>>>>
>>>>> x <- 1400+ 0:10
>>>>> print(dpois(x, 1000), digits =18) ## standard R's double precision
>>>> [1] 1.46677334419659338e-33 1.04694742626454156e-33 7.46752800474106016e-34
>>>> [4] 5.32254312525935864e-34 3.79098513195210765e-34 2.69821005832831136e-34
>>>> [7] 1.91906832029070091e-34 1.36394336907638670e-34 9.68709779173582432e-35
>>>> [10] 6.87515812046484244e-35 4.87599866699657026e-35
>>>>> dpois(mpfr(x, 120), 1000)## more accuracy for the same
>>>>
>>>> *** caught illegal operation ***
>>>> address 0x10a6e1c42, cause 'illegal opcode'
>>>>
>>>> Traceback:
>>>> 1: .class1(object)
>>>> 2: as(value, dataClass)
>>>> 3: setDataPart(x, .Call(Math_mpfr, x, .Math.codes[[.Generic]]))
>>>> 4: exp(-lambda)
>>>> 5: exp(-lambda)
>>>> 6: dpois(mpfr(x, 120), 1000)
>>>>
>>>> Possible actions:
>>>> 1: abort (with core dump, if enabled)
>>>> 2: normal R exit
>>>> 3: exit R without saving workspace
>>>> 4: exit R saving workspace
>>>>
>>>> </(in+output)
>>>>
>>>> Other trials seem to experience similar issues.
>>>>
>>>>
>>>> regards
>>>>
>>>> Berend
>>>>
>>>> _______________________________________________
>>>> R-SIG-Mac mailing list
>>>> R-SIG-Mac@r-project.org
>>>> https://stat.ethz.ch/mailman/listinfo/r-sig-mac
>>>
>>>
>>>
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