Rtools44

a <- c("NA", NA, "BANANA")
na <- NA_character_
a1 <- substr(a,1,1)
stopifnot(is.na(a1)==is.na(a))
a2 <- substring(a,1,1)
stopifnot(is.na(a2)==is.na(a))
a3 <- sub("NA","na",a)
stopifnot(is.na(a3)==is.na(a))
a3 <- gsub("NA","na",a)
stopifnot(is.na(a3)==is.na(a))
substr(a3, 1, 2) <- "na"
stopifnot(is.na(a3)==is.na(a))
substr(a3, 1, 2) <- na
stopifnot(all(is.na(a3)))
stopifnot(agrep("NA", a) == c(1, 3))

Hello, Tomas.

I ran check again and this time it failed on base. Base failed at
"agrep" and utils failed at "adist" if that triggers any ideas.

Thank you,

Avi

On Mon, Mar 18, 2024 at 11:49?PM Avraham Adler <avraham.adler at gmail.com> wrote:

Hello, Tomas.

I had hoped that my problem was that I was linking to OpenBLAS built
under Rtools43, but sadly that is not the case, as I built OpenBLAS
using Rtools44 and I still get the error in 'utils'. I do have
Rtools43 installed on this machine, but I am doing eveything from the
Rtools44 bash. My MkRules.local follows:

USE_ATLAS = YES
ATLAS_PATH = C:/R/OPB/OPB_03.26_1T_44
EOPTS = -march=native -pipe -mno-rtm
LTO = -flto=1 -fuse-linker-plugin
LTO_OPT = -flto=1 -fuse-linker-plugin
LTO_FC = -flto=1 -fuse-linker-plugin
LTO_FC_OPT = -flto=1 -fuse-linker-plugin
QPDF = C:/R/qpdf-11.9.0-msvc64
OPENMP = -fopenmp

I also make the following change to Makefile.win in /src/extra/blas as
I have been doing for more than a decade:

--- /c/r/trunk/src/extra/blas/Makefile.win    2024-01-24
18:34:42.755255900 +0000
+++ /c/r/Makefile.win    2024-01-24 18:39:39.716458000 +0000
@@ -12,7 +12,7 @@
 ../../../$(BINDIR)/Rblas.dll: blas00.o ../../gnuwin32/dllversion.o
     @$(ECHO) -------- Building $@ --------
     $(DLL) -s -shared $(DLLFLAGS) -o $@ $^ Rblas.def \
-       -L../../../$(IMPDIR) -lR  -L"$(ATLAS_PATH)" -lf77blas -latlas
+       -L../../../$(IMPDIR) -lR -L"$(ATLAS_PATH)" -fopenmp -lopenblas
 else
 ../../../$(BINDIR)/Rblas.dll: blas.o blas2.o cmplxblas.o cmplxblas2.o
../../gnuwin32/dllversion.o
     @$(ECHO) -------- Building $@ --------

The utils-Ex.Rout.fail is 1188 lines long and I don't see any obvious
point of failure. The last few lines are:

cleanEx()
nameEx("adist")
### * adist

flush(stderr()); flush(stdout())

### Name: adist
### Title: Approximate String Distances
### Aliases: adist
### Keywords: character

### ** Examples

## Cf. https://en.wikipedia.org/wiki/Levenshtein_distance
adist("kitten", "sitting")

     [,1]
[1,]    3

## To see the transformation counts for the Levenshtein distance:
drop(attr(adist("kitten", "sitting", counts = TRUE), "counts"))

ins del sub
  1   0   2

## To see the transformation sequences:
attr(adist(c("kitten", "sitting"), counts = TRUE), "trafos")

     [,1]      [,2]
[1,] "MMMMMM"  "SMMMSMI"
[2,] "SMMMSMD" "MMMMMMM"

## Cf. the examples for agrep:
adist("lasy", "1 lazy 2")

     [,1]
[1,]    5

## For a "partial approximate match" (as used for agrep):
adist("lasy", "1 lazy 2", partial = TRUE)

The build works under Rtools43. Should I uninstall both versions of
Rtools, my current R installation, and its library and try again? I'm
doubtful that will help as my "active" R installation is in a
completely different directory, but I am willing to try. If there is
any output or other tests I can do, please let me know. Or, if you
think I should raise this on r-devel.

Thank you,

Avi

On Mon, Mar 18, 2024 at 4:08?AM Tomas Kalibera <tomas.kalibera at gmail.com> wrote:

Hello Avi,

On 3/17/24 17:53, Avraham Adler wrote:

Hello, Tomas.

As always, thank you for your incessant hard work. I have compiled
R-devel 86144 using Rtools44 and it completes normally. However, it
fails very early in make check-devel. Specifically, I get the output
below, and have received it more than once. Is this something to raise
on R-devel or is it an Rtools44-specific issue?

I can't tell from this output. Could you please try to get a more
specific error output?
Could you please share your compiler options (e.g. MkRules.local) and
indeed if you made any modifications to the code?

Also, as always, it is worth making sure that all code has been rebuilt
using the new Rtools - e.g. delete any old package library for R-devel
(4.4) you may have on your system.

The testing done by myself and CRAN only covers the default compilation
options as specified in the make files.

Best
Tomas

Thank you,

Avi

$ make check-devel
Testing examples for package 'base'
Testing examples for package 'tools'
   comparing 'tools-Ex.Rout' to 'tools-Ex.Rout.save' ... NOTE
   1046,1047d1045
   < Warning in file(con, "r") :
   <   file("") only supports open = "w+" and open = "w+b": using the former
   1050,1051c1048,1049
   <  $ file    : chr ""
   <  $ title   : chr ""
   ---

   >  $ file    : chr "grid.Rnw"
   >  $ title   : chr "Introduction to grid"

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:208: test-Examples] Error 2
make[1]: *** [Makefile.common:193: test-all-basics] Error 1
make: *** [Makefile:333: check-devel] Error 2



On Thu, Mar 14, 2024 at 4:45?AM Tomas Kalibera <tomas.kalibera at gmail.com> wrote:

Dear R Windows developers,

there is now a new toolchain for R for Windows, Rtools44. It is now used
by R-devel and is intended for R 4.4.0.

Compared to Rtools43, it uses GCC 13 and updates other core components.
See https://cran.r-project.org/bin/windows/Rtools/rtools44/news.html for
a detailed list of changes.

All users of R-devel who need to compile R packages with source code in
C, C++ or Fortran should install Rtools44. From the user perspective,
Rtools44 works the same way as Rtools43. See
https://cran.r-project.org/bin/windows/base/howto-R-devel.html for
instructions on how to build R-devel and packages for this version of R.

It is recommended to re-install packages that need compilation to avoid
potential incompatibilities with code built using Rtools43.

Rtools44 also includes an experimental version for 64-bit ARM machines,
using LLVM 17 (and clang, flang-new, lld, libc++) - the aarch64 version
of Rtools has its own installer and distribution tarballs.

Best
Tomas