INLA on Alpine linux
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Thierry Onkelinx
Oct 9, 2025, 4:03:50 AM (5 days ago) Oct 9
to R-inla discussion group
Dear all,
I'm trying to run INLA on Alpine linux because it is a minimal distribution, leading to much smaller Docker images (about 1 GB smaller than an Ubuntu based Docker).
However, I'm getting the error that "inla.mkl" is not found. Below is a Dockerfile to reproduce the problem and the commands to build and run it.
> INLA::inla(mpg ~ wt, family = "gaussian", data = mtcars)
readlink: unrecognized option: e
BusyBox v1.37.0 (2025-08-05 16:40:33 UTC) multi-call binary.
Usage: readlink [-fnv] FILE
Display the value of a symlink
-n Don't add newline
-f Canonicalize by following all symlinks
-v Verbose
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 90: /root/inla.mkl: No such file or directory
*** inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1
readlink: unrecognized option: e
BusyBox v1.37.0 (2025-08-05 16:40:33 UTC) multi-call binary.
Usage: readlink [-fnv] FILE
Display the value of a symlink
-n Don't add newline
-f Canonicalize by following all symlinks
-v Verbose
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 90: /root/inla.mkl: No such file or directory
Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, :
The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
If this does not help, please contact the developers at <he...@r-inla.org>.
The inla program failed and the maximum number of tries has been reached.
Calls: <Anonymous> -> inla.core.safe
Execution halted
readlink: unrecognized option: e
BusyBox v1.37.0 (2025-08-05 16:40:33 UTC) multi-call binary.
Usage: readlink [-fnv] FILE
Display the value of a symlink
-n Don't add newline
-f Canonicalize by following all symlinks
-v Verbose
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 90: /root/inla.mkl: No such file or directory
*** inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1
readlink: unrecognized option: e
BusyBox v1.37.0 (2025-08-05 16:40:33 UTC) multi-call binary.
Usage: readlink [-fnv] FILE
Display the value of a symlink
-n Don't add newline
-f Canonicalize by following all symlinks
-v Verbose
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 90: /root/inla.mkl: No such file or directory
Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, :
The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
If this does not help, please contact the developers at <he...@r-inla.org>.
The inla program failed and the maximum number of tries has been reached.
Calls: <Anonymous> -> inla.core.safe
Execution halted
##### Dockerfile
FROM rhub/r-minimal:4.5.1-patched
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org/", INLA = "https://inla.r-inla-download.org/R/stable"))' > /usr/local/lib/R/etc/Rprofile.site
# install minimal dependencies
RUN installr -c -p -a 'gfortran icu-data-full linux-headers' fmesher lifecycle rlang withr MatrixModels
# install INLA
RUN Rscript -e 'install.packages("INLA")'
CMD R -e 'INLA::inla(mpg ~ wt, family = "gaussian", data = mtcars)'
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org/", INLA = "https://inla.r-inla-download.org/R/stable"))' > /usr/local/lib/R/etc/Rprofile.site
# install minimal dependencies
RUN installr -c -p -a 'gfortran icu-data-full linux-headers' fmesher lifecycle rlang withr MatrixModels
# install INLA
RUN Rscript -e 'install.packages("INLA")'
CMD R -e 'INLA::inla(mpg ~ wt, family = "gaussian", data = mtcars)'
##### Dockerfile
# Build docker
docker build --tag inla-test .
# Run docker
docker run --rm inla-test
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry....@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry....@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
Postadres: Koning Albert II-laan 15 bus 186, 1210 Brussel
Poststukken die naar dit adres worden gestuurd, worden ingescand en digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar dossiers volledig digitaal behandelen. Poststukken met de vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde bezorgd.
www.inbo.be
Poststukken die naar dit adres worden gestuurd, worden ingescand en digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar dossiers volledig digitaal behandelen. Poststukken met de vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde bezorgd.
www.inbo.be
///////////////////////////////////////////////////////////////////////////////////////////
To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////
INLA help
Oct 9, 2025, 4:08:25 AM (5 days ago) Oct 9
to R-inla discussion group, Thierry Onkelinx
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 90: /root/inla.mkl: No such file or directory
This is where it happens. Add after the first line of ‘inla.mkl.run’,
set -vx
So we can see in the output what is happening.
set -vx
So we can see in the output what is happening.
—
Haavard Rue
HelpDesk
help@r-inla. org
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Thierry Onkelinx
Oct 9, 2025, 4:45:09 AM (5 days ago) Oct 9
to INLA help, R-inla discussion group
Dear Havard,
Here is the output you requested. I started R from the directory containing inla.mkl.run.
I used the testing version of INLA. You can find the session info at the end of the output.
Best regards,
Thierry
> INLA::inla(mpg ~ wt, family = "gaussian", data = mtcars)
cmd=$(readlink -e "$0")
++ readlink -e /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
++ readlink -e /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
readlink: unrecognized option: e
BusyBox v1.37.0 (2025-08-05 16:40:33 UTC) multi-call binary.
Usage: readlink [-fnv] FILE
Display the value of a symlink
-n Don't add newline
-f Canonicalize by following all symlinks
-v Verbose
+ cmd=
DIR=$(dirname "$cmd")
++ dirname ''
+ DIR=.
tmp=$(basename "$0")
++ basename /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ tmp=inla.mkl.run
prog=${tmp%%.run}
+ prog=inla.mkl
DR=""
+ DR=
if [ ! -z ${R_HOME+x} ]; then
d="$R_HOME/lib"
if [ -d "$d" ]; then
DR=$d
fi
fi
+ '[' '!' -z x ']'
+ d=/usr/local/lib/R/lib
+ '[' -d /usr/local/lib/R/lib ']'
+ DR=/usr/local/lib/R/lib
D=""
+ D=
for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib; do
if [ -d "$d" ]; then
if [ -z "$D" ]; then
D="$d"
else
D="$D:$d"
fi
fi
done
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib64 ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib64 ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib64/R/lib ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib/x86_64-linux-gnu ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib/x86_64-linux-gnu ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib ']'
+ '[' -z '' ']'
+ D=/lib
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib ']'
+ '[' -z /lib ']'
+ D=/lib:/usr/lib
if [ -n "${INLA_NATIVE_LD_LIBRARY_PATH}" ]; then
## so we can revert back to old behaviour
export LD_LIBRARY_PATH="$DIR/first:$D:$DIR:$LD_LIBRARY_PATH"
else
## this is the new default, is that we use the libs used when we
## build. Try to use libR from system by default
export LD_LIBRARY_PATH="$DIR/first:$DR:$DIR:$D:$LD_LIBRARY_PATH"
fi
+ '[' -n '' ']'
+ export LD_LIBRARY_PATH=./first:/usr/local/lib/R/lib:.:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ LD_LIBRARY_PATH=./first:/usr/local/lib/R/lib:.:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
export PARDISOLICMESSAGE=1
+ export PARDISOLICMESSAGE=1
+ PARDISOLICMESSAGE=1
if [ -n "${INLA_MALLOC_LIB}" ]; then
if [ -f "${INLA_MALLOC_LIB}" ]; then
export LD_PRELOAD="${INLA_MALLOC_LIB}:$LD_PRELOAD"
else
for nm in ${INLA_MALLOC_LIB}; do
for f in $DIR/malloc/lib*.so*; do
case "$f" in
$DIR/malloc/lib${INLA_MALLOC_LIB}malloc.so*)
export LD_PRELOAD="$f:$LD_PRELOAD";;
esac
done
done
fi
case "$LD_PRELOAD" in
*libjemalloc*)
;;
*libmimalloc*)
;;
esac
fi
+ '[' -n mi ']'
+ '[' -f mi ']'
+ for nm in ${INLA_MALLOC_LIB}
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ export LD_PRELOAD=./malloc/libmimalloc.so.3.0:
+ LD_PRELOAD=./malloc/libmimalloc.so.3.0:
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ case "$LD_PRELOAD" in
if [ -n "${INLA_DEBUG}" ]; then
export OMP_DISPLAY_ENV=true
for var in $(set | grep ^INLA_); do
echo "*** $0 *** $var"
done
echo "*** $0 *** MALLOC_CONF=$MALLOC_CONF"
echo "*** $0 *** LD_PRELOAD=$LD_PRELOAD"
echo "*** $0 *** LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
ldd -r "$DIR/$prog"
for arg in "$@"; do
if [ -r "$arg" ]; then
echo -e "\n*** FILE $arg:"
grep ^### "$arg"
echo -e "*** END OF FILE $arg:\n"
fi
done
fi
+ '[' -n '' ']'
if [ -n "${INLA_DEBUG}" ]; then
set | grep ^OMP_ | while read v; do echo "*** $0 *** $v"; done
echo " *** $0 *** exec $DIR/$prog $@"
fi
+ '[' -n '' ']'
nc=""
+ nc=
if [ -n "$INLA_NUMACTL_ARG" ]; then
ncp=$(type --path numactl)
if [ -n "$ncp" ]; then
nc="$ncp ${INLA_NUMACTL_ARG} "
fi
fi
+ '[' -n '' ']'
exec $nc "$DIR/$prog" "$@"
+ exec ./inla.mkl -s -v -t12:1 -P compact /tmp/RtmpJDbNKl/file118185488b4/Model.ini
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 91: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
DIR=$(dirname "$cmd")
++ dirname ''
+ DIR=.
tmp=$(basename "$0")
++ basename /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ tmp=inla.mkl.run
prog=${tmp%%.run}
+ prog=inla.mkl
DR=""
+ DR=
if [ ! -z ${R_HOME+x} ]; then
d="$R_HOME/lib"
if [ -d "$d" ]; then
DR=$d
fi
fi
+ '[' '!' -z x ']'
+ d=/usr/local/lib/R/lib
+ '[' -d /usr/local/lib/R/lib ']'
+ DR=/usr/local/lib/R/lib
D=""
+ D=
for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib; do
if [ -d "$d" ]; then
if [ -z "$D" ]; then
D="$d"
else
D="$D:$d"
fi
fi
done
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib64 ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib64 ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib64/R/lib ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib/x86_64-linux-gnu ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib/x86_64-linux-gnu ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib ']'
+ '[' -z '' ']'
+ D=/lib
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib ']'
+ '[' -z /lib ']'
+ D=/lib:/usr/lib
if [ -n "${INLA_NATIVE_LD_LIBRARY_PATH}" ]; then
## so we can revert back to old behaviour
export LD_LIBRARY_PATH="$DIR/first:$D:$DIR:$LD_LIBRARY_PATH"
else
## this is the new default, is that we use the libs used when we
## build. Try to use libR from system by default
export LD_LIBRARY_PATH="$DIR/first:$DR:$DIR:$D:$LD_LIBRARY_PATH"
fi
+ '[' -n '' ']'
+ export LD_LIBRARY_PATH=./first:/usr/local/lib/R/lib:.:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ LD_LIBRARY_PATH=./first:/usr/local/lib/R/lib:.:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
export PARDISOLICMESSAGE=1
+ export PARDISOLICMESSAGE=1
+ PARDISOLICMESSAGE=1
if [ -n "${INLA_MALLOC_LIB}" ]; then
if [ -f "${INLA_MALLOC_LIB}" ]; then
export LD_PRELOAD="${INLA_MALLOC_LIB}:$LD_PRELOAD"
else
for nm in ${INLA_MALLOC_LIB}; do
for f in $DIR/malloc/lib*.so*; do
case "$f" in
$DIR/malloc/lib${INLA_MALLOC_LIB}malloc.so*)
export LD_PRELOAD="$f:$LD_PRELOAD";;
esac
done
done
fi
case "$LD_PRELOAD" in
*libjemalloc*)
;;
*libmimalloc*)
;;
esac
fi
+ '[' -n mi ']'
+ '[' -f mi ']'
+ for nm in ${INLA_MALLOC_LIB}
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ export LD_PRELOAD=./malloc/libmimalloc.so.3.0:
+ LD_PRELOAD=./malloc/libmimalloc.so.3.0:
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ case "$LD_PRELOAD" in
if [ -n "${INLA_DEBUG}" ]; then
export OMP_DISPLAY_ENV=true
for var in $(set | grep ^INLA_); do
echo "*** $0 *** $var"
done
echo "*** $0 *** MALLOC_CONF=$MALLOC_CONF"
echo "*** $0 *** LD_PRELOAD=$LD_PRELOAD"
echo "*** $0 *** LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
ldd -r "$DIR/$prog"
for arg in "$@"; do
if [ -r "$arg" ]; then
echo -e "\n*** FILE $arg:"
grep ^### "$arg"
echo -e "*** END OF FILE $arg:\n"
fi
done
fi
+ '[' -n '' ']'
if [ -n "${INLA_DEBUG}" ]; then
set | grep ^OMP_ | while read v; do echo "*** $0 *** $v"; done
echo " *** $0 *** exec $DIR/$prog $@"
fi
+ '[' -n '' ']'
nc=""
+ nc=
if [ -n "$INLA_NUMACTL_ARG" ]; then
ncp=$(type --path numactl)
if [ -n "$ncp" ]; then
nc="$ncp ${INLA_NUMACTL_ARG} "
fi
fi
+ '[' -n '' ']'
exec $nc "$DIR/$prog" "$@"
+ exec ./inla.mkl -s -v -t12:1 -P compact /tmp/RtmpJDbNKl/file118185488b4/Model.ini
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 91: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
*** inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1
cmd=$(readlink -e "$0")
++ readlink -e /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
++ readlink -e /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
readlink: unrecognized option: e
BusyBox v1.37.0 (2025-08-05 16:40:33 UTC) multi-call binary.
Usage: readlink [-fnv] FILE
Display the value of a symlink
-n Don't add newline
-f Canonicalize by following all symlinks
-v Verbose
+ cmd=
DIR=$(dirname "$cmd")
++ dirname ''
+ DIR=.
tmp=$(basename "$0")
++ basename /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ tmp=inla.mkl.run
prog=${tmp%%.run}
+ prog=inla.mkl
DR=""
+ DR=
if [ ! -z ${R_HOME+x} ]; then
d="$R_HOME/lib"
if [ -d "$d" ]; then
DR=$d
fi
fi
+ '[' '!' -z x ']'
+ d=/usr/local/lib/R/lib
+ '[' -d /usr/local/lib/R/lib ']'
+ DR=/usr/local/lib/R/lib
D=""
+ D=
for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib; do
if [ -d "$d" ]; then
if [ -z "$D" ]; then
D="$d"
else
D="$D:$d"
fi
fi
done
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib64 ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib64 ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib64/R/lib ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib/x86_64-linux-gnu ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib/x86_64-linux-gnu ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib ']'
+ '[' -z '' ']'
+ D=/lib
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib ']'
+ '[' -z /lib ']'
+ D=/lib:/usr/lib
if [ -n "${INLA_NATIVE_LD_LIBRARY_PATH}" ]; then
## so we can revert back to old behaviour
export LD_LIBRARY_PATH="$DIR/first:$D:$DIR:$LD_LIBRARY_PATH"
else
## this is the new default, is that we use the libs used when we
## build. Try to use libR from system by default
export LD_LIBRARY_PATH="$DIR/first:$DR:$DIR:$D:$LD_LIBRARY_PATH"
fi
+ '[' -n '' ']'
+ export LD_LIBRARY_PATH=./first:/usr/local/lib/R/lib:.:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ LD_LIBRARY_PATH=./first:/usr/local/lib/R/lib:.:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
export PARDISOLICMESSAGE=1
+ export PARDISOLICMESSAGE=1
+ PARDISOLICMESSAGE=1
if [ -n "${INLA_MALLOC_LIB}" ]; then
if [ -f "${INLA_MALLOC_LIB}" ]; then
export LD_PRELOAD="${INLA_MALLOC_LIB}:$LD_PRELOAD"
else
for nm in ${INLA_MALLOC_LIB}; do
for f in $DIR/malloc/lib*.so*; do
case "$f" in
$DIR/malloc/lib${INLA_MALLOC_LIB}malloc.so*)
export LD_PRELOAD="$f:$LD_PRELOAD";;
esac
done
done
fi
case "$LD_PRELOAD" in
*libjemalloc*)
;;
*libmimalloc*)
;;
esac
fi
+ '[' -n mi ']'
+ '[' -f mi ']'
+ for nm in ${INLA_MALLOC_LIB}
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ export LD_PRELOAD=./malloc/libmimalloc.so.3.0:
+ LD_PRELOAD=./malloc/libmimalloc.so.3.0:
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ case "$LD_PRELOAD" in
if [ -n "${INLA_DEBUG}" ]; then
export OMP_DISPLAY_ENV=true
for var in $(set | grep ^INLA_); do
echo "*** $0 *** $var"
done
echo "*** $0 *** MALLOC_CONF=$MALLOC_CONF"
echo "*** $0 *** LD_PRELOAD=$LD_PRELOAD"
echo "*** $0 *** LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
ldd -r "$DIR/$prog"
for arg in "$@"; do
if [ -r "$arg" ]; then
echo -e "\n*** FILE $arg:"
grep ^### "$arg"
echo -e "*** END OF FILE $arg:\n"
fi
done
fi
+ '[' -n '' ']'
if [ -n "${INLA_DEBUG}" ]; then
set | grep ^OMP_ | while read v; do echo "*** $0 *** $v"; done
echo " *** $0 *** exec $DIR/$prog $@"
fi
+ '[' -n '' ']'
nc=""
+ nc=
if [ -n "$INLA_NUMACTL_ARG" ]; then
ncp=$(type --path numactl)
if [ -n "$ncp" ]; then
nc="$ncp ${INLA_NUMACTL_ARG} "
fi
fi
+ '[' -n '' ']'
exec $nc "$DIR/$prog" "$@"
+ exec ./inla.mkl -s -v -t12:1 -P compact /tmp/RtmpJDbNKl/file1182d16734f/Model.ini
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 91: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
DIR=$(dirname "$cmd")
++ dirname ''
+ DIR=.
tmp=$(basename "$0")
++ basename /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ tmp=inla.mkl.run
prog=${tmp%%.run}
+ prog=inla.mkl
DR=""
+ DR=
if [ ! -z ${R_HOME+x} ]; then
d="$R_HOME/lib"
if [ -d "$d" ]; then
DR=$d
fi
fi
+ '[' '!' -z x ']'
+ d=/usr/local/lib/R/lib
+ '[' -d /usr/local/lib/R/lib ']'
+ DR=/usr/local/lib/R/lib
D=""
+ D=
for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib; do
if [ -d "$d" ]; then
if [ -z "$D" ]; then
D="$d"
else
D="$D:$d"
fi
fi
done
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib64 ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib64 ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib64/R/lib ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib/x86_64-linux-gnu ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib/x86_64-linux-gnu ']'
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /lib ']'
+ '[' -z '' ']'
+ D=/lib
+ for d in {,/usr}/lib64 /usr/lib64/R/lib {,/usr}/lib/x86_64-linux-gnu {,/usr}/lib
+ '[' -d /usr/lib ']'
+ '[' -z /lib ']'
+ D=/lib:/usr/lib
if [ -n "${INLA_NATIVE_LD_LIBRARY_PATH}" ]; then
## so we can revert back to old behaviour
export LD_LIBRARY_PATH="$DIR/first:$D:$DIR:$LD_LIBRARY_PATH"
else
## this is the new default, is that we use the libs used when we
## build. Try to use libR from system by default
export LD_LIBRARY_PATH="$DIR/first:$DR:$DIR:$D:$LD_LIBRARY_PATH"
fi
+ '[' -n '' ']'
+ export LD_LIBRARY_PATH=./first:/usr/local/lib/R/lib:.:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ LD_LIBRARY_PATH=./first:/usr/local/lib/R/lib:.:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
export PARDISOLICMESSAGE=1
+ export PARDISOLICMESSAGE=1
+ PARDISOLICMESSAGE=1
if [ -n "${INLA_MALLOC_LIB}" ]; then
if [ -f "${INLA_MALLOC_LIB}" ]; then
export LD_PRELOAD="${INLA_MALLOC_LIB}:$LD_PRELOAD"
else
for nm in ${INLA_MALLOC_LIB}; do
for f in $DIR/malloc/lib*.so*; do
case "$f" in
$DIR/malloc/lib${INLA_MALLOC_LIB}malloc.so*)
export LD_PRELOAD="$f:$LD_PRELOAD";;
esac
done
done
fi
case "$LD_PRELOAD" in
*libjemalloc*)
;;
*libmimalloc*)
;;
esac
fi
+ '[' -n mi ']'
+ '[' -f mi ']'
+ for nm in ${INLA_MALLOC_LIB}
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ export LD_PRELOAD=./malloc/libmimalloc.so.3.0:
+ LD_PRELOAD=./malloc/libmimalloc.so.3.0:
+ for f in $DIR/malloc/lib*.so*
+ case "$f" in
+ case "$LD_PRELOAD" in
if [ -n "${INLA_DEBUG}" ]; then
export OMP_DISPLAY_ENV=true
for var in $(set | grep ^INLA_); do
echo "*** $0 *** $var"
done
echo "*** $0 *** MALLOC_CONF=$MALLOC_CONF"
echo "*** $0 *** LD_PRELOAD=$LD_PRELOAD"
echo "*** $0 *** LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
ldd -r "$DIR/$prog"
for arg in "$@"; do
if [ -r "$arg" ]; then
echo -e "\n*** FILE $arg:"
grep ^### "$arg"
echo -e "*** END OF FILE $arg:\n"
fi
done
fi
+ '[' -n '' ']'
if [ -n "${INLA_DEBUG}" ]; then
set | grep ^OMP_ | while read v; do echo "*** $0 *** $v"; done
echo " *** $0 *** exec $DIR/$prog $@"
fi
+ '[' -n '' ']'
nc=""
+ nc=
if [ -n "$INLA_NUMACTL_ARG" ]; then
ncp=$(type --path numactl)
if [ -n "$ncp" ]; then
nc="$ncp ${INLA_NUMACTL_ARG} "
fi
fi
+ '[' -n '' ']'
exec $nc "$DIR/$prog" "$@"
+ exec ./inla.mkl -s -v -t12:1 -P compact /tmp/RtmpJDbNKl/file1182d16734f/Model.ini
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 91: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, :
The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
If this does not help, please contact the developers at <he...@r-inla.org>.
The inla program failed and the maximum number of tries has been reached.
> sessioninfo::session_info("INLA")
─ Session info ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────setting value
version R version 4.5.1 Patched (2025-09-24 r88906)
os Alpine Linux v3.22
system x86_64, linux-musl
ui unknown
language (EN)
collate C
ctype C.UTF-8
tz UTC
date 2025-10-09
pandoc NA
quarto NA
─ Packages ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
class 7.3-23 2025-01-01 [1] CRAN (R 4.5.1)
classInt 0.4-11 2025-01-08 [1] CRAN (R 4.5.1)
cli 3.6.5 2025-04-23 [1] CRAN (R 4.5.1)
DBI 1.2.3 2024-06-02 [1] CRAN (R 4.5.1)
dplyr 1.1.4 2023-11-17 [1] CRAN (R 4.5.1)
e1071 1.7-16 2024-09-16 [1] CRAN (R 4.5.1)
fmesher 0.5.0 2025-07-07 [1] CRAN (R 4.5.1)
generics 0.1.4 2025-05-09 [1] CRAN (R 4.5.1)
glue 1.8.0 2024-09-30 [1] CRAN (R 4.5.1)
INLA 25.10.01 2025-10-01 [1] local
KernSmooth 2.23-26 2025-01-01 [1] CRAN (R 4.5.1)
lattice 0.22-7 2025-04-02 [1] CRAN (R 4.5.1)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.5.1)
magrittr 2.0.4 2025-09-12 [1] CRAN (R 4.5.1)
MASS 7.3-65 2025-02-28 [1] CRAN (R 4.5.1)
Matrix 1.7-4 2025-08-28 [1] CRAN (R 4.5.1)
MatrixModels 0.5-4 2025-03-26 [1] CRAN (R 4.5.1)
pillar 1.11.1 2025-09-17 [1] CRAN (R 4.5.1)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.5.1)
proxy 0.4-27 2022-06-09 [1] CRAN (R 4.5.1)
R6 2.6.1 2025-02-15 [1] CRAN (R 4.5.1)
Rcpp 1.1.0 2025-07-02 [1] CRAN (R 4.5.1)
rlang 1.1.6 2025-04-11 [1] CRAN (R 4.5.1)
s2 1.1.9 2025-05-23 [1] CRAN (R 4.5.1)
sf 1.0-21 2025-05-15 [1] CRAN (R 4.5.1)
sp 2.2-0 2025-02-01 [1] CRAN (R 4.5.1)
splancs 2.01-45 2024-05-27 [1] CRAN (R 4.5.1)
tibble 3.3.0 2025-06-08 [1] CRAN (R 4.5.1)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.5.1)
units 0.8-7 2025-03-11 [1] CRAN (R 4.5.1)
utf8 1.2.6 2025-06-08 [1] CRAN (R 4.5.1)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.5.1)
withr 3.0.2 2024-10-28 [1] CRAN (R 4.5.1)
wk 0.9.4 2024-10-11 [1] CRAN (R 4.5.1)
[1] /usr/local/lib/R/library
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry....@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry....@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
Postadres: Koning Albert II-laan 15 bus 186, 1210 Brussel
Poststukken die naar dit adres worden gestuurd, worden ingescand en digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar dossiers volledig digitaal behandelen. Poststukken met de vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde bezorgd.
www.inbo.be
Poststukken die naar dit adres worden gestuurd, worden ingescand en digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar dossiers volledig digitaal behandelen. Poststukken met de vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde bezorgd.
www.inbo.be
///////////////////////////////////////////////////////////////////////////////////////////
To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
///////////////////////////////////////////////////////////////////////////////////////////
Op do 9 okt 2025 om 10:08 schreef INLA help <he...@r-inla.org>:
Facundo Muñoz
Oct 9, 2025, 5:10:22 AM (5 days ago) Oct 9
to r-inla-disc...@googlegroups.com
Hi Thierry,
Part of the problem seems to be that INLA is relying in GNU version of `readlink`, while alpine ships a striped-down version [1].
Still, installing GNU coreutils beforehand does not solve the problem completely. Now I get a different error:
aa5dfcfd5292:~# Rscript -e 'INLA::inla(mpg ~ wt, family =
"gaussian", data = mtcars)'
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line
90: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot
execute: required file not found
*** inla.core.safe: The inla program failed, but will rerun in
case better initial values may help. try=1/1
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 90: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
Error in inla.core.safe(formula = formula, family = family,
contrasts = contrasts, :
The inla-program exited with an error. Unless you interupted it
yourself, please rerun with verbose=TRUE and check the output
carefully.
If this does not help, please contact the developers at
<he...@r-inla.org>.
The inla program failed and the maximum number of tries has been
reached.
Calls: <Anonymous> -> inla.core.safe
Execution halted
Helpdesk (Haavard Rue)
Oct 9, 2025, 5:22:05 AM (5 days ago) Oct 9
to Facundo Muñoz, r-inla-disc...@googlegroups.com
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 91:
installation error
can you add after 'set -vx'
ls -lR /usr/local/lib/R/library/INLA/bin
we can replace 'readline -f' with a shell function, like below, although its
annoying that these issues arise. MacOS has the same issue for older versions of
MacOS (now its fine). this code is from old versions of the `run' script, but
can be adapted to check if '-f' is supported or not (or just replace it
entirely)
if [ "$(type --path readlink)"X == "X" ]; then
readlink () {
(
shift 1
tfile=$1
cd $(dirname "$tfile")
tfile=$(basename "$tfile")
while [ -L "$tfile" ]
do
tfile=$(readlink -f "$tfile")
cd $(dirname "$tfile")
tfile=$(basename "$tfile")
done
pdir=$(pwd -P)
echo "$pdir/$tfile"
)
}
fi
> .
--
Håvard Rue
he...@r-inla.org
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required
file not found
which says that the main executable file is not there, so there must be some
file not found
installation error
can you add after 'set -vx'
ls -lR /usr/local/lib/R/library/INLA/bin
we can replace 'readline -f' with a shell function, like below, although its
annoying that these issues arise. MacOS has the same issue for older versions of
MacOS (now its fine). this code is from old versions of the `run' script, but
can be adapted to check if '-f' is supported or not (or just replace it
entirely)
if [ "$(type --path readlink)"X == "X" ]; then
readlink () {
(
shift 1
tfile=$1
cd $(dirname "$tfile")
tfile=$(basename "$tfile")
while [ -L "$tfile" ]
do
tfile=$(readlink -f "$tfile")
cd $(dirname "$tfile")
tfile=$(basename "$tfile")
done
pdir=$(pwd -P)
echo "$pdir/$tfile"
)
}
fi
> > --
> > You received this message because you are subscribed to the Google Groups
> > "R-inla discussion group" group.
> > To unsubscribe from this group and stop receiving emails from it, send an
> > email to r-inla-discussion...@googlegroups.com.
> > To view this discussion, visit
> > https://groups.google.com/d/msgid/r-inla-discussion-group/CAJuCY5wcCR72r%2BQYgnHNL6RuA3W5TqEsUWesKpe-HsMHmbHFNQ%40mail.gmail.com
> > .
> >
>
>
> --
> You received this message because you are subscribed to the Google Groups "R-
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> To unsubscribe from this group and stop receiving emails from it, send an
> email to r-inla-discussion...@googlegroups.com.
> To view this discussion, visit
> https://groups.google.com/d/msgid/r-inla-discussion-group/f69b264d-186b-49eb-8e79-c28ab590ac69%40gmail.com
> > You received this message because you are subscribed to the Google Groups
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> > To unsubscribe from this group and stop receiving emails from it, send an
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> > To view this discussion, visit
> > https://groups.google.com/d/msgid/r-inla-discussion-group/CAJuCY5wcCR72r%2BQYgnHNL6RuA3W5TqEsUWesKpe-HsMHmbHFNQ%40mail.gmail.com
> > .
> >
>
>
> --
> You received this message because you are subscribed to the Google Groups "R-
> inla discussion group" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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> To view this discussion, visit
> .
--
Håvard Rue
he...@r-inla.org
Thierry Onkelinx
Oct 9, 2025, 6:17:44 AM (5 days ago) Oct 9
to Helpdesk, Facundo Muñoz, r-inla-disc...@googlegroups.com
Dear Havard,
Here is the updated Dockerfile and output. The new docker installs co
### Dockerfile
FROM rhub/r-minimal:4.5.1-patched
RUN apk add nano
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org/", INLA = "https://inla.r-inla-download.org/R/testing"))' > /usr/local/lib/R/etc/Rprofile.site
# install minimal dependencies
RUN installr -c -p -a 'coreutils gfortran icu-data-full linux-headers' fmesher lifecycle rlang withr MatrixModels sessioninfo
RUN apk add nano
RUN echo 'options(repos = c(CRAN = "https://cloud.r-project.org/", INLA = "https://inla.r-inla-download.org/R/testing"))' > /usr/local/lib/R/etc/Rprofile.site
# install minimal dependencies
RUN installr -c -p -a 'coreutils gfortran icu-data-full linux-headers' fmesher lifecycle rlang withr MatrixModels sessioninfo
# install INLA
RUN Rscript -e 'install.packages("INLA")'
COPY fix.sh fix.sh
CMD R -e 'sessioninfo::session_info("INLA")' -e 'INLA::inla(mpg ~ wt, family = "gaussian", data = mtcars)'
CMD R -e 'sessioninfo::session_info("INLA")' -e 'INLA::inla(mpg ~ wt, family = "gaussian", data = mtcars)'
### Dockerfile
### fix.sh
sed -i.bak '2i\
set -vx\
' /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
sed -i.bak '3i\
ls -lR /usr/local/lib/R/library/INLA/bin\
' /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
set -vx\
' /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
sed -i.bak '3i\
ls -lR /usr/local/lib/R/library/INLA/bin\
' /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
### fix.sh
───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
> INLA::inla(mpg ~ wt, family = "gaussian", data = mtcars)
ls -lR /usr/local/lib/R/library/INLA/bin
+ ls -lR /usr/local/lib/R/library/INLA/bin
+ ls -lR /usr/local/lib/R/library/INLA/bin
cmd=$(readlink -e "$0")
++ readlink -e /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ cmd=/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
DIR=$(dirname "$cmd")
++ dirname /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ DIR=/usr/local/lib/R/library/INLA/bin/linux/64bit
DIR=$(dirname "$cmd")
++ dirname /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ DIR=/usr/local/lib/R/library/INLA/bin/linux/64bit
+ export LD_LIBRARY_PATH=/usr/local/lib/R/library/INLA/bin/linux/64bit/first:/usr/local/lib/R/lib:/usr/local/lib/R/library/INLA/bin/linux/64bit:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ LD_LIBRARY_PATH=/usr/local/lib/R/library/INLA/bin/linux/64bit/first:/usr/local/lib/R/lib:/usr/local/lib/R/library/INLA/bin/linux/64bit:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ LD_LIBRARY_PATH=/usr/local/lib/R/library/INLA/bin/linux/64bit/first:/usr/local/lib/R/lib:/usr/local/lib/R/library/INLA/bin/linux/64bit:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ export LD_PRELOAD=/usr/local/lib/R/library/INLA/bin/linux/64bit/malloc/libmimalloc.so.3.0:
+ LD_PRELOAD=/usr/local/lib/R/library/INLA/bin/linux/64bit/malloc/libmimalloc.so.3.0:
+ LD_PRELOAD=/usr/local/lib/R/library/INLA/bin/linux/64bit/malloc/libmimalloc.so.3.0:
+ exec /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl -s -v -t12:1 -P compact /tmp/RtmpkbEpLH/filea18bbbfd/Model.ini
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 94: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 94: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
*** inla.core.safe: The inla program failed, but will rerun in case better initial values may help. try=1/1
ls -lR /usr/local/lib/R/library/INLA/bin
+ ls -lR /usr/local/lib/R/library/INLA/bin
+ ls -lR /usr/local/lib/R/library/INLA/bin
cmd=$(readlink -e "$0")
++ readlink -e /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ cmd=/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
DIR=$(dirname "$cmd")
++ dirname /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ DIR=/usr/local/lib/R/library/INLA/bin/linux/64bit
DIR=$(dirname "$cmd")
++ dirname /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run
+ DIR=/usr/local/lib/R/library/INLA/bin/linux/64bit
+ export LD_LIBRARY_PATH=/usr/local/lib/R/library/INLA/bin/linux/64bit/first:/usr/local/lib/R/lib:/usr/local/lib/R/library/INLA/bin/linux/64bit:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ LD_LIBRARY_PATH=/usr/local/lib/R/library/INLA/bin/linux/64bit/first:/usr/local/lib/R/lib:/usr/local/lib/R/library/INLA/bin/linux/64bit:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ LD_LIBRARY_PATH=/usr/local/lib/R/library/INLA/bin/linux/64bit/first:/usr/local/lib/R/lib:/usr/local/lib/R/library/INLA/bin/linux/64bit:/lib:/usr/lib:/usr/local/lib/R/lib:/usr/local/lib
+ export LD_PRELOAD=/usr/local/lib/R/library/INLA/bin/linux/64bit/malloc/libmimalloc.so.3.0:
+ LD_PRELOAD=/usr/local/lib/R/library/INLA/bin/linux/64bit/malloc/libmimalloc.so.3.0:
+ LD_PRELOAD=/usr/local/lib/R/library/INLA/bin/linux/64bit/malloc/libmimalloc.so.3.0:
+ exec /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl -s -v -t12:1 -P compact /tmp/RtmpkbEpLH/filea3a0bba81/Model.ini
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 94: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
/usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl.run: line 94: /usr/local/lib/R/library/INLA/bin/linux/64bit/inla.mkl: cannot execute: required file not found
Error in inla.core.safe(formula = formula, family = family, contrasts = contrasts, :
The inla-program exited with an error. Unless you interupted it yourself, please rerun with verbose=TRUE and check the output carefully.
If this does not help, please contact the developers at <he...@r-inla.org>.
The inla program failed and the maximum number of tries has been reached.
Calls: <Anonymous> -> inla.core.safe
Execution halted
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry....@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry....@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
Postadres: Koning Albert II-laan 15 bus 186, 1210 Brussel
Poststukken die naar dit adres worden gestuurd, worden ingescand en digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar dossiers volledig digitaal behandelen. Poststukken met de vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde bezorgd.
www.inbo.be
Poststukken die naar dit adres worden gestuurd, worden ingescand en digitaal aan de geadresseerde bezorgd. Zo kan de Vlaamse overheid haar dossiers volledig digitaal behandelen. Poststukken met de vermelding ‘vertrouwelijk’ worden niet ingescand, maar ongeopend aan de geadresseerde bezorgd.
www.inbo.be
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To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. ~ John Tukey
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Op do 9 okt 2025 om 11:22 schreef Helpdesk (Haavard Rue) <he...@r-inla.org>:
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