[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 14:35:37 CET 2020
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
[[alternative HTML version deleted]]
More information about the R-package-devel
mailing list