=> Bootstrap dependency digest>=20010302: found digest-20190127
===> Skipping vulnerability checks.
WARNING: No /var/db/pkg/pkg-vulnerabilities file found.
WARNING: To fix run: `/usr/sbin/pkg_admin -K /var/db/pkg fetch-pkg-vulnerabilities'.
===> Installing for R-3.6.0
=> 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-3.6.0/m4'
gmake[1]: Nothing to be done for 'install'.
gmake[1]: Leaving directory '/tmp/math/R/work/R-3.6.0/m4'
gmake[1]: Entering directory '/tmp/math/R/work/R-3.6.0/tools'
gmake[1]: Nothing to be done for 'install'.
gmake[1]: Leaving directory '/tmp/math/R/work/R-3.6.0/tools'
gmake[1]: Entering directory '/tmp/math/R/work/R-3.6.0/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-3.6.0/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-3.6.0/doc/html'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/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-3.6.0/doc/manual'
gmake[1]: Leaving directory '/tmp/math/R/work/R-3.6.0/doc'
gmake[1]: Entering directory '/tmp/math/R/work/R-3.6.0/etc'
mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/etc
installing etc ...
gmake[1]: Leaving directory '/tmp/math/R/work/R-3.6.0/etc'
gmake[1]: Entering directory '/tmp/math/R/work/R-3.6.0/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-3.6.0/share'
gmake[1]: Entering directory '/tmp/math/R/work/R-3.6.0/src'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/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-3.6.0/src/scripts'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/src/include'
mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/include
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/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-3.6.0/src/include/R_ext'
gmake[2]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/include'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/src/extra'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/extra/blas'
gmake[3]: Nothing to be done for 'install'.
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/extra/blas'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/extra/tre'
gmake[3]: Nothing to be done for 'install'.
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/extra/tre'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/extra/tzone'
gmake[3]: Nothing to be done for 'install'.
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/extra/tzone'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/extra/xdr'
gmake[3]: Nothing to be done for 'install'.
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/extra/xdr'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/extra/intl'
gmake[3]: Nothing to be done for 'install'.
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/extra/intl'
gmake[2]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/extra'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/src/appl'
gmake[2]: Nothing to be done for 'install'.
gmake[2]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/appl'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/src/nmath'
gmake[2]: Nothing to be done for 'install'.
gmake[2]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/nmath'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/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/X11R7/include/freetype2 -I/usr/X11R7/include/libdrm -I/usr/include/krb5 -DHAVE_CONFIG_H    -O2 -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/X11R7/include/freetype2 -I/usr/X11R7/include/libdrm -I/usr/include/krb5  -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-3.6.0/src/unix'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/src/main'
mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/bin/exec
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/main'
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/main'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/main'
mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/lib
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/main'
gmake[2]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/main'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/src/modules'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/modules/internet'
mkdir /tmp/math/R/work/.destdir/usr/pkg/lib/R/modules
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/modules/internet'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/modules/lapack'
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/modules/lapack'
gmake[3]: Entering directory '/tmp/math/R/work/R-3.6.0/src/modules/X11'
gmake[3]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/modules/X11'
gmake[2]: Leaving directory '/tmp/math/R/work/R-3.6.0/src/modules'
gmake[2]: Entering directory '/tmp/math/R/work/R-3.6.0/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-3.6.0/src/library'
gmake[1]: Leaving directory '/tmp/math/R/work/R-3.6.0/src'
gmake[1]: Entering directory '/tmp/math/R/work/R-3.6.0/tests'
gmake[1]: Nothing to be done for 'install'.
gmake[1]: Leaving directory '/tmp/math/R/work/R-3.6.0/tests'
gmake[1]: Entering directory '/tmp/math/R/work/R-3.6.0/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-3.6.0/doc/manual'
=> Automatic manual page handling
=> Generating post-install file lists
=> Checking file-check results for R-3.6.0
=> Checking for non-existent script interpreters in R-3.6.0
=> Checking file permissions in R-3.6.0
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.
warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/library/rpart/help/figures/rpart.png: executable bit is set on non-executable file.
warning: /tmp/math/R/work/.destdir/usr/pkg/lib/R/library/survival/NEWS.Rd: executable bit is set on non-executable file.
0 errors and 21 warnings.
=> Checking for missing run-time search paths in R-3.6.0
WARNING: Skipping check for SSP in DESTDIR mode.
=> Checking for work-directory references in R-3.6.0
ERROR: /usr/pkg/lib/R/etc/Makeconf:	# configure  '--enable-R-shlib' '--with-readline' '--with-lapack' '--with-tcltk' '--with-tcl-config=/usr/pkg/lib/tclConfig.sh' '--with-tk-config=/usr/pkg/lib/tkConfig.sh' '--without-gnome' '--with-system-zlib' '--with-system-bzlib' '--with-system-pcre' '--with-system-xz' '--enable-long-double=no' '--with-x' '--without-atlas' '--disable-BLAS-shlib' '--with-blas' '--without-blas_risc' '--without-dxml' '--without-libmoto' '--x-includes=/usr/X11R7/include' '--x-libraries=/usr/X11R7/lib' '--with-libiconv-prefix=/usr/pkg' '--prefix=/usr/pkg' '--build=x86_64--netbsd' '--host=x86_64--netbsd' '--infodir=/usr/pkg/info' '--mandir=/usr/pkg/man' '--enable-option-checking=yes' 'build_alias=x86_64--netbsd' 'host_alias=x86_64--netbsd' 'R_PAPERSIZE=A4' 'MAKE=make' 'TAR=/bin/tar' 'LIBnn=lib' 'PKG_CONFIG=/tmp/math/R/work/.tools/bin/pkg-config' 'PKG_CONFIG_PATH=' 'PKG_CONFIG_LIBDIR=/tmp/math/R/work/.buildlink/lib/pkgconfig:/tmp/math/R/work/.buildlink/share/pkgconfig' 'CC=gcc' 'CFLAGS=-O2 -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/X11R7/include/freetype2 -I/usr/X11R7/include/libdrm -I/usr/include/krb5' 'LDFLAGS=-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' 'LIBS=' 'CPPFLAGS=-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/X11R7/include/freetype2 -I/usr/X11R7/include/libdrm -I/usr/include/krb5' 'FC=g95' 'CXX=c++' 'CXXFLAGS=-O2 -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/X11R7/include/freetype2 -I/usr/X11R7/include/libdrm -I/usr/include/krb5' 'XMKMF=/usr/pkg/bin/xmkmf'
ERROR: *** The above files still have references to the build directory.
ERROR:     This is possibly an error that should be fixed by unwrapping
ERROR:     the files or adding missing tools to the package makefile!
*** 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