Re: wip/R has 4.3.1, please check

[Chavdar Ivanov <ci4ic4%gmail.com@localhost>]

On Sat, 8 Jul 2023 at 07:11, Thomas Klausner <wiz%netbsd.org@localhost> wrote:
>
> On Sat, Jul 08, 2023 at 08:42:35AM +0900, Makoto Fujiwara wrote:
> >
> > | To: pkgsrc-users%NetBSD.org@localhost
> > | From: Thomas Klausner <wiz%NetBSD.org@localhost>
> > | Subject: math/R: link issue
> > | Date: Fri, 7 Jul 2023 00:31:01 +0200
> > | Message-ID: <ZKdApWpPbf99a6Pz%yt.nih.at@localhost>
> > > On the other hand, 4.2.3 and 4.3.1 are out (pkgsrc is at 4.2.0), so if
> > > someone feels like updating math/R that'd be nice too :)
> >   ..
> > >  Thomas
> >
> > wip/R has 4.3.1, please check it if you have time, thanks
>
> Thank you!
>
> For me, it fails the same way:
>
> gmake[3]: Entering directory '/scratch/wip/R/work/R-4.3.1/src/main'
> gcc -I../../src/extra  -I. -I../../src/include -I../../src/include -I/usr/pkg/include -g -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5 -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -g -fPIC -D_FORTIFY_SOURCE=2 -fstack-clash-protection -pthread -I/usr/include -I/usr/pkg/include -I/usr/pkg/include/glib-2.0 -I/usr/pkg/include/gio-unix-2.0 -I/usr/pkg/lib/glib-2.0/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5  -c Rmain.c -o Rmain.o
> gcc -Wl,--export-dynamic -fopenmp  -Wl,-R/usr/pkg/lib/R/lib -L"../../lib" -Wl,-zrelro -Wl,-znow -L/usr/lib -Wl,-R/usr/lib -L/usr/pkg/lib -Wl,-R/usr/pkg/lib -pthread -o R.bin Rmain.o  -lR
> ld: warning: libgomp.so.1, needed by ../../lib/libR.so, may conflict with libgomp.so.2
> ld: ../../lib/libR.so: undefined reference to `textdomain'
> ld: ../../lib/libR.so: undefined reference to `dgettext'
> ld: ../../lib/libR.so: undefined reference to `dngettext'
> ld: ../../lib/libR.so: undefined reference to `gettext'
> ld: ../../lib/libR.so: undefined reference to `ngettext'
> ld: ../../lib/libR.so: undefined reference to `bindtextdomain'
> gmake[3]: *** [Makefile:150: R.bin] Error 1
> gmake[3]: Leaving directory '/scratch/wip/R/work/R-4.3.1/src/main'
> gmake[2]: *** [Makefile:141: R] Error 2
>
>  Thomas

Same here, but I can build it using

 gcc -Wl,--export-dynamic -fopenmp  -Wl,-R/usr/pkg/lib/R/lib
-L"../../lib" -Wl,-zrelro -L/usr/lib -L/usr/pkg/lib -Wl,-R/usr/lib
-Wl,-R/usr/pkg/lib -pthread -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib
-lintl -o R.bin Rmain.o  -lR

then it completes (albeit for some reason further configure not
finding jni.h from openjdk17, even if the command line specifies
correctly the location).

The resulting executable is also not usable for the exact reason
mentioned in the other thread:

 ldd /usr/pkg/lib/R/bin/exec/R
/usr/pkg/lib/R/bin/exec/R:
        -lintl.1 => /usr/lib/libintl.so.1    <--------------
        -lc.12 => /usr/lib/libc.so.12
        -lR => /usr/pkg/lib/R/lib/libR.so
        -lblas.3 => /usr/pkg/lib/libblas.so.3
        -lgfortran.5 => /usr/pkg/gcc10//lib/./libgfortran.so.5
        -lquadmath.0 => /usr/pkg/gcc10//lib/./libquadmath.so.0
        -lm.0 => /usr/lib/libm.so.0
        -lgcc_s.1 => /usr/lib/libgcc_s.so.1
        -lpthread.1 => /usr/lib/libpthread.so.1
        -lintl.8 => /usr/pkg/lib/libintl.so.8 <----------------------
        -lreadline.8 => /usr/pkg/lib/libreadline.so.8
        -lterminfo.2 => /usr/lib/libterminfo.so.2
        -lpcre2-8.0 => /usr/pkg/lib/libpcre2-8.so.0
        -llzma.2 => /usr/lib/liblzma.so.2
        -lbz2.1 => /usr/lib/libbz2.so.1
        -lz.1 => /usr/lib/libz.so.1
        -lrt.1 => /usr/lib/librt.so.1
        -liconv.2 => /usr/pkg/lib/libiconv.so.2
        -lgomp.1 => /usr/pkg/gcc10//lib/./libgomp.so.1
        -lgomp.2 => /usr/lib/libgomp.so.2

(demo() crashes the same way).




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