=> Bootstrap dependency digest>=20211023: found digest-20220214 ===> Skipping vulnerability checks. WARNING: No /usr/pkg/pkgdb/pkg-vulnerabilities file found. WARNING: To fix run: `/usr/sbin/pkg_admin -K /usr/pkg/pkgdb fetch-pkg-vulnerabilities'. ===> Installing for R-4.4.2nb3 => Generating pre-install file lists mkdir /tmp/math/R/work/.destdir/usr/pkg/lib mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R gmake[1]: Entering directory '/tmp/math/R/work/R-4.4.2/m4' gmake[1]: Nothing to be done for 'install'. gmake[1]: Leaving directory '/tmp/math/R/work/R-4.4.2/m4' gmake[1]: Entering directory '/tmp/math/R/work/R-4.4.2/tools' gmake[1]: Nothing to be done for 'install'. gmake[1]: Leaving directory '/tmp/math/R/work/R-4.4.2/tools' gmake[1]: Entering directory '/tmp/math/R/work/R-4.4.2/doc' installing doc ... mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/doc mkdir /tmp/math/R/work/.destdir/usr/pkg/man mkdir /tmp/math/R/work/.destdir/usr/pkg/man/man1 gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/doc/html' installing doc/html ... mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/doc/html gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/doc/html' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/doc/manual' installing doc/manual ... mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/doc/manual mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/doc/manual/images gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/doc/manual' gmake[1]: Leaving directory '/tmp/math/R/work/R-4.4.2/doc' gmake[1]: Entering directory '/tmp/math/R/work/R-4.4.2/etc' mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/etc installing etc ... gmake[1]: Leaving directory '/tmp/math/R/work/R-4.4.2/etc' gmake[1]: Entering directory '/tmp/math/R/work/R-4.4.2/share' installing share ... mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/R mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/dictionaries mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/encodings mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/java mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/licenses mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/make mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/Rd mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/Rd/macros mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/sh mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/texmf mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/texmf/bibtex mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/texmf/bibtex/bib mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/texmf/bibtex/bst mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/texmf/tex mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/share/texmf/tex/latex gmake[1]: Leaving directory '/tmp/math/R/work/R-4.4.2/share' gmake[1]: Entering directory '/tmp/math/R/work/R-4.4.2/src' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/scripts' mkdir /tmp/math/R/work/.destdir/usr/pkg/bin mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/scripts' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/include' mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/include gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/include/R_ext' mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/include/R_ext gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/include/R_ext' gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/include' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/extra' gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/extra/blas' gmake[3]: Nothing to be done for 'install'. gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/extra/blas' gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/extra/tre' gmake[3]: Nothing to be done for 'install'. gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/extra/tre' gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/extra/tzone' gmake[3]: Nothing to be done for 'install'. gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/extra/tzone' gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/extra/xdr' gmake[3]: Nothing to be done for 'install'. gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/extra/xdr' gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/extra' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/appl' gmake[2]: Nothing to be done for 'install'. gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/appl' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/nmath' gmake[2]: Nothing to be done for 'install'. gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/nmath' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/unix' gcc -I. -I../../src/include -I../../src/include -I/usr/X11R7/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 -DHAVE_CONFIG_H -O2 -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 -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 -DR_HOME='"/usr/pkg/lib/R"' \ -o Rscript ./Rscript.c mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/pkgconfig gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/unix' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/main' mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/exec gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/main' gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/main' gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/main' mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/lib gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/main' gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/main' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/modules' gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/modules/internet' mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/modules gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/modules/internet' gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/modules/lapack' gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/modules/lapack' gmake[3]: Entering directory '/tmp/math/R/work/R-4.4.2/src/modules/X11' gmake[3]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/modules/X11' gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/modules' gmake[2]: Entering directory '/tmp/math/R/work/R-4.4.2/src/library' mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/library installing packages ... building HTML index ... gmake[2]: Leaving directory '/tmp/math/R/work/R-4.4.2/src/library' gmake[1]: Leaving directory '/tmp/math/R/work/R-4.4.2/src' gmake[1]: Entering directory '/tmp/math/R/work/R-4.4.2/tests' gmake[1]: Nothing to be done for 'install'. gmake[1]: Leaving directory '/tmp/math/R/work/R-4.4.2/tests' gmake[1]: Entering directory '/tmp/math/R/work/R-4.4.2/doc/manual' mkdir /tmp/math/R/work/.destdir/usr/pkg/info /usr/bin/install -c -m 644 "./dir" "/tmp/math/R/work/.destdir/usr/pkg/info" installing R info pages ... updating '/usr/pkg/info/dir' ... gmake[1]: Leaving directory '/tmp/math/R/work/R-4.4.2/doc/manual' /bin/rm -f /tmp/math/R/work/.destdir/usr/pkg/lib/R/library/survival/NEWS.Rd.orig => Automatic manual page handling => Generating post-install file lists => Checking file-check results for R-4.4.2nb3 => Checking for non-existent script interpreters in R-4.4.2nb3 => Checking file permissions in R-4.4.2nb3 warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/BATCH: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/COMPILE: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/INSTALL: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/LINK: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/REMOVE: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/Rd2pdf: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/Rdconv: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/Rdiff: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/Rprof: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/SHLIB: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/Stangle: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/Sweave: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/build: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/check: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/config: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/javareconf: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/rtags: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/library/foreign/files/sids.dbf: executable bit is set on non-executable file. warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/library/mgcv/CITATION: executable bit is set on non-executable file. 0 errors and 19 warnings. => Checking for PIE in R-4.4.2nb3 => Checking for RELRO in R-4.4.2nb3 => Checking for missing run-time search paths in R-4.4.2nb3 ERROR: lib/R/bin/exec/R: missing library: libR.so ERROR: lib/R/library/KernSmooth/libs/KernSmooth.so: missing library: libR.so ERROR: lib/R/library/MASS/libs/MASS.so: missing library: libR.so ERROR: lib/R/library/Matrix/libs/Matrix.so: missing library: libR.so ERROR: lib/R/library/class/libs/class.so: missing library: libR.so ERROR: lib/R/library/cluster/libs/cluster.so: missing library: libR.so ERROR: lib/R/library/foreign/libs/foreign.so: missing library: libR.so ERROR: lib/R/library/grDevices/libs/cairo.so: missing library: libR.so ERROR: lib/R/library/grDevices/libs/grDevices.so: missing library: libR.so ERROR: lib/R/library/graphics/libs/graphics.so: missing library: libR.so ERROR: lib/R/library/grid/libs/grid.so: missing library: libR.so ERROR: lib/R/library/lattice/libs/lattice.so: missing library: libR.so ERROR: lib/R/library/methods/libs/methods.so: missing library: libR.so ERROR: lib/R/library/mgcv/libs/mgcv.so: missing library: libR.so ERROR: lib/R/library/nlme/libs/nlme.so: missing library: libR.so ERROR: lib/R/library/nnet/libs/nnet.so: missing library: libR.so ERROR: lib/R/library/parallel/libs/parallel.so: missing library: libR.so ERROR: lib/R/library/rpart/libs/rpart.so: missing library: libR.so ERROR: lib/R/library/spatial/libs/spatial.so: missing library: libR.so ERROR: lib/R/library/splines/libs/splines.so: missing library: libR.so ERROR: lib/R/library/stats/libs/stats.so: missing library: libR.so ERROR: lib/R/library/survival/libs/survival.so: missing library: libR.so ERROR: lib/R/library/tcltk/libs/tcltk.so: missing library: libR.so ERROR: lib/R/library/tools/libs/tools.so: missing library: libR.so ERROR: lib/R/library/utils/libs/utils.so: missing library: libR.so ERROR: lib/R/modules/R_X11.so: missing library: libR.so ERROR: lib/R/modules/R_de.so: missing library: libR.so ERROR: lib/R/modules/internet.so: missing library: libR.so ERROR: lib/R/modules/lapack.so: missing library: libR.so *** Error code 1 Stop. make[1]: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/math/R *** Error code 1 Stop. make: stopped in /amd/pkgsrc/CHROOT/P/pkgsrc/math/R