[R-pkg-devel] Errors in make check in Windows 10 with OpenBLAS
Erin Hodgess
er|nm@hodge@@ @end|ng |rom gm@||@com
Sat Mar 21 17:38:34 CET 2020
Thanks!
I searched the output for Riconv but no luck yet.
On Sat, Mar 21, 2020 at 10:29 AM Tomas Kalibera <tomas.kalibera using gmail.com>
wrote:
> Maybe the created Riconv.dll is copied over by libiconv at some point
> during your custom build.
>
> Tomas
>
> On 3/21/20 3:58 PM, Erin Hodgess wrote:
>
> Hello again.
>
> So I'm trying to find the place where the GNU iconv comes from. However,
> I looked at output from both the regular build and the custom, and I'm not
> seeing any differences in how win_iconv is generated.
>
> Any suggestions, please?
>
> Custom:
> c:/Rtools/mingw_64/bin/ar crs libtz.a localtime.o registryTZ.o strftime.o
> installing zoneinfo
> making win_iconv.d from win_iconv.c
> c:/Rtools/mingw_64/bin/gcc -std=gnu99 -I../../include -O3 -Wall
> -pedantic -march=native -pipe -c win_iconv.c -o win_iconv.o
> c:/Rtools/mingw_64/bin/gcc -std=gnu99 -shared -o Riconv.dll Riconv.def
> win_iconv.o
>
> Regular:
> c:/Rtools/mingw_64/bin/ar crs libtz.a localtime.o registryTZ.o strftime.o
> installing zoneinfo
> making win_iconv.d from win_iconv.c
> c:/Rtools/mingw_64/bin/gcc -std=gnu99 -I../../include -O3 -Wall
> -pedantic -mtune=core2 -c win_iconv.c -o win_iconv.o
> c:/Rtools/mingw_64/bin/gcc -std=gnu99 -shared -o Riconv.dll Riconv.def
> win_iconv.o
>
> Just the -march=native -pipe
>
> Erin Hodgess, PhD
> mailto: erinm.hodgess using gmail.com
>
>
> On Fri, Mar 20, 2020 at 9:01 AM Tomas Kalibera <tomas.kalibera using gmail.com>
> wrote:
>
>> Thanks, so the problem is that your custom build uses GNU libiconv, which
>> does not support codepage 28605. win_iconv, the one shipped with R,
>> supports that code page. win_iconv is a wrapper for the Windows API. Unless
>> you had a special reason not to, I would just recommend to use win_iconv.
>> The "experience" will match the C library conversion calls, which may be
>> used directly in some code at some places, and it is most tested as people
>> normally use it. Still, the problem is not specific to strtrim, just to the
>> example.
>>
>> Best
>> Tomas
>>
>>
>> On 3/20/20 3:27 PM, Erin Hodgess wrote:
>>
>> Here are the results.
>>
>> Looks like enc2native and the iconv settings are different.
>>
>>
>> > #output from custom build
>> > Sys.getlocale()
>> [1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252"
>> > enc2native("\uff21")
>> [1] "<U+FF21>"
>> > enc2native("\u4e2d")
>> [1] "<U+4E2D>"
>> > Sys.setlocale("LC_CTYPE", "English_United States.28605")
>> [1] "English_United States.28605"
>> > enc2native("\uff21")
>> Error: unsupported conversion from 'UTF-8' in codepage 28605
>> > enc2native("\u4e2d")
>> Error: unsupported conversion from 'UTF-8' in codepage 28605
>> > extSoftVersion()[c("iconv","BLAS")]
>> iconv BLAS
>> "GNU libiconv 1.14" ""
>>
>>
>> > #output from regular build
>> > Sys.getlocale()
>> [1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United
>> States.1252;LC_MONETARY=English_United
>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252"
>> > enc2native("\uff21")
>> [1] "A"
>> > enc2native("\u4e2d")
>> [1] "<U+4E2D>"
>> > Sys.setlocale("LC_CTYPE", "English_United States.28605")
>> [1] "English_United States.28605"
>> > enc2native("\uff21")
>> [1] "A"
>> > enc2native("\u4e2d")
>> [1] "<U+4E2D>"
>> > extSoftVersion()[c("iconv","BLAS")]
>> iconv BLAS
>> "win_iconv" ""
>> >
>>
>> Thanks!
>>
>>
>> Erin Hodgess, PhD
>> mailto: erinm.hodgess using gmail.com
>>
>>
>> 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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