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ReproNim
AFNI build failing because R_io.so target fails
I am trying to build AFNI from source, master branch.
make[1]: Leaving directory '/opt/afni-master/src/ptaylor'
echo PKG_CPPFLAGS = -I. -I/usr/include -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -DHAVE_ZLIB -DHAVE_GIFTI -If2c > Makevars ; \
echo PKG_LIBS = -L. -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -lmri -lf2c -lXm -lXt -lXft -lXp -lXpm -lfontconfig -lXext -lXmu -lSM -lICE -lX11 -lpng -ljpeg -lz -lexpat -lm -ldl -lc >> Makevars ;
( if which R >/dev/null ; then \
R CMD SHLIB -o R_io.so R_io.c ; \
else echo WARNING: Cannot build R_io.so because R is not installed;\
fi ; )
make[1]: Entering directory '/opt/afni-master/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I. -I/usr/include -Inifti/nifti2 -Inifti/niftilib -Inifti/nifticdf -Inifti/znzlib -I3DEdge/src -Irickr -DHAVE_ZLIB -DHAVE_GIFTI -If2c -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c R_io.c -o R_io.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o R_io.so R_io.o -L. -L/usr/lib64 -L/usr/lib/x86_64-linux-gnu -lmri -lf2c -lXm -lXt -lXft -lXp -lXpm -lfontconfig -lXext -lXmu -lSM -lICE -lX11 -lpng -ljpeg -lz -lexpat -lm -ldl -lc -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lXp
/usr/bin/ld: cannot find -lXmu
collect2: error: ld returned 1 exit status
/usr/share/R/share/make/shlib.mk:6: recipe for target 'R_io.so' failed
make[1]: *** [R_io.so] Error 1
make[1]: Leaving directory '/opt/afni-master/src'
Makefile.INCLUDE:3995: recipe for target 'R_io.so' failed
make: *** [R_io.so] Error 1
FATAL: failed to execute %post proc: exit status 2
FATAL: While performing build: while running engine: while running /usr/libexec/singularity/bin/starter: exit status 255
I've been trying to install AFNI version 2011_12_21_1014 and had to make a few changes, including solving this issue. After a bit of trial and error, I ended up with this. I'm not sure why I had to do a second apt-get install to get those libraries to "stick" but it worked for building on Ubuntu 16. (Note: I made all the chained commands separate RUN calls to ease debugging.)
# Generated by: Neurodocker version 0.7.0
# Timestamp: 2021/03/30 18:36:31 UTC
#
# Thank you for using Neurodocker. If you discover any issues
# or ways to improve this software, please submit an issue or
# pull request on our GitHub repository:
#
# https://github.com/ReproNim/neurodocker
FROM ubuntu:16.04
USER root
ARG DEBIAN_FRONTEND="noninteractive"
ENV LANG="en_US.UTF-8" \
LC_ALL="en_US.UTF-8" \
ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN export ND_ENTRYPOINT="/neurodocker/startup.sh"
RUN apt-get update -qq
RUN apt-get install -y -q --no-install-recommends \
apt-utils \
bzip2 \
ca-certificates \
curl \
locales \
unzip
RUN sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen
RUN dpkg-reconfigure --frontend=noninteractive locales
RUN update-locale LANG="en_US.UTF-8"
RUN chmod 777 /opt && chmod a+s /opt
RUN mkdir -p /neurodocker
RUN if [ ! -f "$ND_ENTRYPOINT" ]; then \
echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
&& echo 'set -e' >> "$ND_ENTRYPOINT" \
&& echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
&& echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
fi
RUN chmod -R 777 /neurodocker && chmod a+s /neurodocker
ENTRYPOINT ["/neurodocker/startup.sh"]
ENV PATH="/opt/afni-2011_12_21_1014:$PATH" \
AFNI_PLUGINPATH="/opt/afni-2011_12_21_1014"
RUN apt-get update -qq
RUN apt-get install -y -q --no-install-recommends \
curl \
ed \
g++ \
gcc \
git \
libglib2.0-dev \
libglu1-mesa-dev \
libgsl-dev \
libmotif-dev \
libnetpbm10-dev \
libnlopt-dev \
libxext-dev \
libxi-dev \
libxmu-headers \
libxpm-dev \
libxt-dev \
m4 \
make \
mesa-common-dev \
python \
r-base \
r-base-dev \
tcsh \
zlib1g-dev
RUN curl -sSL --retry 5 -o /tmp/toinstall.deb http://mirrors.kernel.org/debian/pool/main/libx/libxp/libxp6_1.0.2-2_amd64.deb
RUN dpkg -i /tmp/toinstall.deb
RUN rm /tmp/toinstall.deb
RUN curl -sSL --retry 5 -o /tmp/toinstall.deb http://snapshot.debian.org/archive/debian-security/20160113T213056Z/pool/updates/main/libp/libpng/libpng12-0_1.2.49-1%2Bdeb7u2_amd64.deb
RUN dpkg -i /tmp/toinstall.deb
RUN rm /tmp/toinstall.deb
RUN apt-get install -f -y
RUN apt-get install -y -q --no-install-recommends \
libxmu-dev \ # <--- provides the Xmu.h in Ubuntu 16
r-cran-rcpp \ # <--- provides the Xp.h
libglw1-mesa-dev # <--- provides GL/GLwDrawA.h for SUMA
RUN git clone https://github.com/afni/afni.git /opt/afni-2011_12_21_1014
WORKDIR /opt/afni-2011_12_21_1014
RUN git checkout dab76581b2ddef36dd4d5974f122e9759732c5c5 # <--- the git treeish for version 2011_12_21_1014 🙄
WORKDIR /opt/afni-2011_12_21_1014/src
RUN cp Makefile.linux_ubuntu_16_64 Makefile # <--- neurodebian _insists_ on using the wrong Makefile for Ubuntu
RUN make INSTALLDIR="/opt/afni-2011_12_21_1014" vastness
RUN /opt/afni-2011_12_21_1014/rPkgsInstall -pkgs ALL
# Finally, clean up
RUN apt-get clean # <--- remove these lines from above because they will force you
RUN rm -rf /var/lib/apt/lists/* # to run `apt-get update` before EVERY `apt-get install`
WORKDIR /opt/afni-2011_12_21_1014
USER root
RUN echo '{ \
\n "pkg_manager": "apt", \
\n "instructions": [ \
\n [ \
\n "base", \
\n "ubuntu:16.04" \
\n ], \
\n [ \
\n "afni", \
\n { \
\n "version": "latest", \
\n "method": "source", \
\n "install_r": "true", \
\n "install_r_pkgs": "true", \
\n "install_python2": "true", \
\n "install_path": "/opt/afni-2011_12_21_1014" \
\n } \
\n ], \
\n [ \
\n "workdir", \
\n "/opt/afni_2011_12_21_1014" \
\n ], \
\n [ \
\n "user", \
\n "root" \
\n ] \
\n ] \
\n}' > /neurodocker/neurodocker_specs.json
since this is a very old issue, I will close it now, but please reopen if this is still an issue
