[R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS
Erin Hodgess
er|nm@hodge@@ @end|ng |rom gm@||@com
Fri Mar 20 15:04:36 CET 2020
Great idea!
Thanks
On Fri, Mar 20, 2020 at 8:03 AM Tomas Kalibera <tomas.kalibera using gmail.com>
wrote:
> Hi Erin,
>
> when you are building from sources, you can always uncomment the example
> in str.Rd. But it would be good first to find out why it is failing on your
> system/build.
>
> Please run the example in Rgui of the official R 3.6.3 build on your
> machine. Does it work there?
>
> Please run the following commands in Rgui of the official R 3.6.3 build on
> the machine and on your custom build. What do you get?
>
> Sys.getlocale()
> enc2native("\uff21")
> enc2native("\u4e2d")
> Sys.setlocale("LC_CTYPE", "English_United States.28605")
> enc2native("\uff21")
> enc2native("\u4e2d")
> extSoftVersion()[c("iconv","BLAS")]
> Thanks,
> Tomas
>
> On 3/20/20 2:35 PM, Erin Hodgess wrote:
>
> I was wondering if there is a way to either skip the utilities check and
> continuing, in order to test the other packages, please.
>
> Thanks!
>
>
> On Fri, Mar 20, 2020 at 5:01 AM Martin Maechler <
> maechler using stat.math.ethz.ch> wrote:
>
>> >>>>> Erin Hodgess on Thu, 19 Mar 2020 22:44:39 -0600 writes:
>>
>> > Hi Tomas and others:
>> > Here is the session Info. I also used the str example both
>> without and
>> > with changing the locale.
>>
>> > sI <- sessionInfo()
>> >> str(sI)
>> > List of 10
>> > $ R.version :List of 14
>> > ..$ platform : chr "x86_64-w64-mingw32"
>> > ..$ arch : chr "x86_64"
>> > ..$ os : chr "mingw32"
>> > ..$ system : chr "x86_64, mingw32"
>> > ..$ status : chr ""
>> > ..$ major : chr "3"
>> > ..$ minor : chr "6.3"
>> > ..$ year : chr "2020"
>> > ..$ month : chr "02"
>> > ..$ day : chr "29"
>> > ..$ svn rev : chr "77875"
>> > ..$ language : chr "R"
>> > ..$ version.string: chr "R version 3.6.3 (2020-02-29)"
>> > ..$ nickname : chr "Holding the Windsock"
>> > $ platform : chr "x86_64-w64-mingw32/x64 (64-bit)"
>> > $ locale : chr "LC_COLLATE=English_United
>> > States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> > States.125"| __truncated__
>> > $ running : chr "Windows 10 x64 (build 18362)"
>> > $ RNGkind : chr [1:3] "Mersenne-Twister" "Inversion" "Rejection"
>> > $ basePkgs : chr [1:7] "stats" "graphics" "grDevices" "utils" ...
>> > $ loadedOnly:List of 1
>> > ..$ compiler:List of 9
>> > .. ..$ Package : chr "compiler"
>> > .. ..$ Version : chr "3.6.3"
>> > .. ..$ Priority : chr "base"
>> > .. ..$ Title : chr "The R Compiler Package"
>> > .. ..$ Author : chr "Luke Tierney <luke-tierney using uiowa.edu>"
>> > .. ..$ Maintainer : chr "R Core Team <R-core using r-project.org>"
>> > .. ..$ Description: chr "Byte code compiler for R."
>> > .. ..$ License : chr "Part of R 3.6.3"
>> > .. ..$ Built : chr "R 3.6.3; ; 2020-03-20 04:29:00 UTC;
>> windows"
>> > .. ..- attr(*, "class")= chr "packageDescription"
>> > .. ..- attr(*, "file")= chr
>> > "c:/newtimeR/R-3.6.3/library/compiler/Meta/package.rds"
>> > $ matprod : chr "default"
>> > $ BLAS : chr ""
>> > $ LAPACK : chr ""
>> > - attr(*, "class")= chr "sessionInfo"
>>
>>
>> > Running the str example WITHOUT changing the locale:
>> >> ## Truncation behavior (<-> correct width measurement) for "long"
>> > non-ASCII:
>> >> idx <- c(65313:65338, 65345:65350)
>> >> fwch <- intToUtf8(idx) # full width character string: each has
>> width 2
>> >> ch <- strtrim(paste(LETTERS, collapse="._"), 64)
>> >> (ncc <- c(c.ch = nchar(ch), w.ch = nchar(ch, "w"),
>> > + c.fw = nchar(fwch), w.fw = nchar(fwch, "w")))
>> > c.ch w.ch c.fw w.fw
>> > 64 64 32 64
>> >> stopifnot(unname(ncc) == c(64,64, 32, 64))
>> >> ## nchar.max: 1st line needs an increase of 2 in order to see
>> 1 (in
>> > UTF-$
>> >> invisible(lapply(60:66, function(N) str(fwch, nchar.max = N)))
>> > chr "<U+FF21><U+FF22><U+FF23><U+FF24><U+FF25><U+"| __truncated__
>> > chr "<U+FF21><U+FF22><U+FF23><U+FF24><U+FF25><U+F"| __truncated__
>> > chr "<U+FF21><U+FF22><U+FF23><U+FF24><U+FF25><U+FF"| __truncated__
>> > chr "<U+FF21><U+FF22><U+FF23><U+FF24><U+FF25><U+FF2"| __truncated__
>> > chr "<U+FF21><U+FF22><U+FF23><U+FF24><U+FF25><U+FF26"|
>> __truncated__
>> > chr "<U+FF21><U+FF22><U+FF23><U+FF24><U+FF25><U+FF26>"|
>> __truncated__
>> > chr "<U+FF21><U+FF22><U+FF23><U+FF24><U+FF25><U+FF26><"|
>> __truncated__
>> >> invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) #
>> "1 is 1"
>> > he$
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O"| __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O."| __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._"| __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._P"| __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._P."|
>> __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._P._"|
>> __truncated__
>> > chr
>> "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._P._Q._R._S._T._U._V"
>> >>
>>
>> > Running the str example WITH changing the locale:
>>
>> > oloc <- Sys.getlocale("LC_CTYPE")
>> >> mbyte.lc <- if(.Platform$OS.type == "windows")
>> > + "English_United States.28605" else "en_GB.UTF-8"
>> >> try(Sys.setlocale("LC_CTYPE", mbyte.lc))
>> > [1] "English_United States.28605"
>> >> ## Truncation behavior (<-> correct width measurement) for "long"
>> > non-ASCII:
>> >> idx <- c(65313:65338, 65345:65350)
>> >> fwch <- intToUtf8(idx) # full width character string: each has
>> width 2
>> >> ch <- strtrim(paste(LETTERS, collapse="._"), 64)
>> >> (ncc <- c(c.ch = nchar(ch), w.ch = nchar(ch, "w"),
>> > + c.fw = nchar(fwch), w.fw = nchar(fwch, "w")))
>> > c.ch w.ch c.fw w.fw
>> > 64 64 32 64
>> >> stopifnot(unname(ncc) == c(64,64, 32, 64))
>> >> ## nchar.max: 1st line needs an increase of 2 in order to see
>> 1 (in
>> > UTF-$
>> >> invisible(lapply(60:66, function(N) str(fwch, nchar.max = N)))
>> > Error in strtrim(x.lrg, nchar.max - nc) :
>> > unsupported conversion from 'UTF-8' in codepage 28605
>> >> invisible(lapply(60:66, function(N) str( ch , nchar.max = N))) #
>> "1 is 1"
>> > he$
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O"| __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O."| __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._"| __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._P"| __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._P."|
>> __truncated__
>> > chr "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._P._"|
>> __truncated__
>> > chr
>> "A._B._C._D._E._F._G._H._I._J._K._L._M._N._O._P._Q._R._S._T._U._V"
>>
>> > This is pretty strange.
>>
>> It is strange indeed that strtrim() fails in this situation.
>>
>> From what you wrote previously, this only happens when you link
>> with OpenBLAS but not when you use R's own BLAS.
>> Are you sure that that was the only difference, but not rather
>> the difference in the locales you used in your two versions of R
>> on Windows?
>>
>> Martin
>>
>> > Thanks for any help.
>>
>> > Sincerely,
>> > Erin
>>
>> > Erin Hodgess, PhD
>> > mailto: erinm.hodgess using gmail.com
>>
>>
>> > On Thu, Mar 19, 2020 at 2:29 AM Tomas Kalibera <
>> tomas.kalibera using gmail.com>
>> > wrote:
>>
>> >> Hi Erin,
>> >>
>> >> this comes from examples in ?str. Could you please try to find a
>> minimal
>> >> example to reproduce on your system based on that? I would look for
>> >> "line needs" in ?str and experiment with reducing the example there
>> >> while still getting the error. Once it is minimal, could you
>> please try
>> >> also on the official build of R on your machine?
>> >>
>> >> Also it would be nice to have a session info. If it works in the
>> >> official build but not your custom build, then one would have to
>> look
>> >> also into how the custom build is done.
>> >>
>> >> Thanks
>> >> Tomas
>> >>
>> >>
>> >> On 3/19/20 8:02 AM, Erin Hodgess wrote:
>> >> > Hello everyone:
>> >> >
>> >> > I have built the latest version of the OpenBLAS on my Windows 10
>> machine.
>> >> > When I run make distribution in R, everything is fine.
>> >> >
>> >> > However, when I run make check all, I get the following error:
>> >> >
>> >> > C:\newtimeR\R-3.6.3\src\gnuwin32>make check-all
>> >> > Testing examples for package 'base'
>> >> > Testing examples for package 'tools'
>> >> > comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... OK
>> >> > Testing examples for package 'utils'
>> >> > Error: testing 'utils' failed
>> >> > Execution halted
>> >> > make[3]: *** [Makefile.win:29: test-Examples-Base] Error 1
>> >> > make[2]: *** [Makefile.common:185: test-Examples] Error 2
>> >> > make[1]: *** [Makefile.common:171: test-all-basics] Error 1
>> >> > make: *** [Makefile:324: check-all] Error 2
>> >> >
>> >> > And here is the section from the .Rout.fail for utils:
>> >> >
>> >> >> ## Multibyte characters in strings (in multibyte locales):
>> >> >> oloc <- Sys.getlocale("LC_CTYPE")
>> >> >> mbyte.lc <- if(.Platform$OS.type == "windows")
>> >> > + "English_United States.28605" else "en_GB.UTF-8"
>> >> >> try(Sys.setlocale("LC_CTYPE", mbyte.lc))
>> >> > [1] "English_United States.28605"
>> >> >> ## Truncation behavior (<-> correct width measurement) for
>> "long"
>> >> > non-ASCII:
>> >> >> idx <- c(65313:65338, 65345:65350)
>> >> >> fwch <- intToUtf8(idx) # full width character string: each has
>> width 2
>> >> >> ch <- strtrim(paste(LETTERS, collapse="._"), 64)
>> >> >> (ncc <- c(c.ch = nchar(ch), w.ch = nchar(ch, "w"),
>> >> > + c.fw = nchar(fwch), w.fw = nchar(fwch, "w")))
>> >> > c.ch w.ch c.fw w.fw
>> >> > 64 64 32 64
>> >> >> stopifnot(unname(ncc) == c(64,64, 32, 64))
>> >> >> ## nchar.max: 1st line needs an increase of 2 in order to
>> see 1 (in
>> >> > UTF-8!):
>> >> >> invisible(lapply(60:66, function(N) str(fwch, nchar.max = N)))
>> >> > Error in strtrim(x.lrg, nchar.max - nc) :
>> >> > unsupported conversion from 'UTF-8' in codepage 28605
>> >> > Calls: lapply ... FUN -> str -> str.default -> maybe_truncate ->
>> strtrim
>> >> > Execution halted
>> >> >
>> >> > Has anyone run into this before, please?
>> >> >
>> >> > If I run this line-by-line starting at the "idx <-", things are
>> fine.
>> >> >
>> >> > I also compiled R from source without the OpenBLAS, and it was
>> fine.
>> >> >
>> >> > Thanks for any suggestions.
>> >> >
>> >> > Sincerely,
>> >> > Erin
>> >> >
>> >> >
>> >> >
>> >> > Erin Hodgess, PhD
>> >> > mailto: erinm.hodgess using gmail.com
>>
>> --
> Erin Hodgess, PhD
> mailto: erinm.hodgess using gmail.com
>
>
> --
Erin Hodgess, PhD
mailto: erinm.hodgess using gmail.com
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