[R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS

#output from custom build
Sys.getlocale()

enc2native("\uff21")

enc2native("\u4e2d")

Sys.setlocale("LC_CTYPE", "English_United States.28605")

enc2native("\uff21")

enc2native("\u4e2d")

extSoftVersion()[c("iconv","BLAS")]

#output from regular build
Sys.getlocale()

enc2native("\uff21")

enc2native("\u4e2d")

Sys.setlocale("LC_CTYPE", "English_United States.28605")

enc2native("\uff21")

enc2native("\u4e2d")

extSoftVersion()[c("iconv","BLAS")]

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 at 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 at uiowa.edu>"
     > .. ..$ Maintainer : chr "R Core Team <R-core at 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 at gmail.com

     > On Thu, Mar 19, 2020 at 2:29 AM Tomas Kalibera <

tomas.kalibera at 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 at gmail.com

--

Erin Hodgess, PhD
mailto: erinm.hodgess at gmail.com