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

Erin Hodgess er|nm@hodge@@ @end|ng |rom gm@||@com
Sun Mar 22 04:33:34 CET 2020


Finally figured it out...I was having "path problems"!

I'm all set here.

Thanks so much for your help

Sincerely,
Erin

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


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
>>>
>>>
>>>
>>
>

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