Re: math/R: link issue

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

On Thu, 6 Jul 2023 at 23:50, Chavdar Ivanov <ci4ic4%gmail.com@localhost> wrote:
>
> On Thu, 6 Jul 2023 at 23:46, Chavdar Ivanov <ci4ic4%gmail.com@localhost> wrote:
> >
> > Get rid of devel/gettext-lib.
>
> I finished building it - when I got the first message of missing
> symbols, I removed manually all /usr/pkg/lib/libintl* - it continued
> for a while, until it failed because of the lack of those files - so I
> restored them, and it continued up until the end. Weird....

But then I am getting:
...
> demo()

 *** caught segfault ***
address 0x610, cause 'memory not mapped'

Traceback:
 1: tolower(x$title)
 2: paste("R", tolower(x$title))
 3: file.show(outFile, delete.file = TRUE, title = paste("R", tolower(x$title)))
 4: print.packageIQR(x)
 5: (function (x, ...) UseMethod("print"))(x)
....

Otherwise, it seems to work.
> >
> > On Thu, 6 Jul 2023 at 23:31, Thomas Klausner <wiz%netbsd.org@localhost> wrote:
> > >
> > > Hi!
> > >
> > > After the gettext-lib update, math/R has stopped building.
> > >
> > > The error looks like this (from mef's build):
> > >
> > > gcc -I../../src/extra  -I. -I../../src/include -I../../src/include -I/usr/pkg/include -I/usr/pkg/include -I/usr/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/X11R7/include -I/usr/pkg/include/freetype2 -I/usr/pkg/include/harfbuzz -I/usr/include/krb5 -I../../src/nmath -DHAVE_CONFIG_H   -fopenmp -fpic  -O2 -fPIC -D_FORTIFY_SOURCE=2 -pthread -I/usr/pkg/include -I/usr/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/X11R7/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 -L/usr/pkg/lib -L/usr/lib -Wl,-R/usr/lib -Wl,-R/usr/pkg/lib -pthread -L/usr/X11R7/lib -Wl,-R/usr/X11R7/lib -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'
> > >
> > > So it looks like libR.so is not linked against libintl.so, which
> > > should provide these symbols.
> > >
> > >
> > > So I added code to do that, and it still failed. Then I added code to
> > > link R.bin against libintl.so directly too, but that doesn't help
> > > either. Now I'm confused.
> > >
> > > 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 -lintl
> > > 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'
> > >
> > > # ldd work/R-4.2.0/src/main/libR.so
> > > work/R-4.2.0/src/main/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
> > >         -lc.12 => /usr/lib/libc.so.12
> > >         -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
> > >
> > > Does anyone have an idea what could be the underlying issue here?
> > >
> > > 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
> >
> >
> >
> > --
> > ----
>
>
>
> --
> ----



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