Hi all,
I tried to install AFNI. In the beginning, I couldn’t use R from the command so I installed the R again through Homebrew. R seems to work. However, I can’t install the R packages needed for AFNI programs. When I installed it, I got several warning messages as below. Thoughts? Thanks!
updating R_LD_LIBRARY_PATH …
Installing package into ‘/Users/amylo/Library/R/4.0/library’
(as ‘lib’ is unspecified)
Warning: dependency ‘cmdstanr’ is not available
also installing the dependencies ‘units’, ‘V8’, ‘gsl’, ‘sf’, ‘rstan’, ‘shinystan’, ‘rtdists’, ‘spdep’
trying URL ‘http://cloud.r-project.org/src/contrib/units_0.7-1.tar.gz’
Content type ‘application/x-gzip’ length 854699 bytes (834 KB)
downloaded 834 KB
trying URL ‘http://cloud.r-project.org/src/contrib/V8_3.4.0.tar.gz’
Content type ‘application/x-gzip’ length 682079 bytes (666 KB)
downloaded 666 KB
trying URL ‘http://cloud.r-project.org/src/contrib/gsl_2.1-6.tar.gz’
Content type ‘application/x-gzip’ length 189794 bytes (185 KB)
downloaded 185 KB
trying URL ‘http://cloud.r-project.org/src/contrib/sf_0.9-8.tar.gz’
Content type ‘application/x-gzip’ length 4213253 bytes (4.0 MB)
downloaded 4.0 MB
trying URL ‘http://cloud.r-project.org/src/contrib/rstan_2.21.2.tar.gz’
Content type ‘application/x-gzip’ length 1152008 bytes (1.1 MB)
downloaded 1.1 MB
trying URL ‘http://cloud.r-project.org/src/contrib/shinystan_2.5.0.tar.gz’
Content type ‘application/x-gzip’ length 2400413 bytes (2.3 MB)
downloaded 2.3 MB
trying URL ‘http://cloud.r-project.org/src/contrib/rtdists_0.11-2.tar.gz’
Content type ‘application/x-gzip’ length 867210 bytes (846 KB)
downloaded 846 KB
trying URL ‘http://cloud.r-project.org/src/contrib/spdep_1.1-7.tar.gz’
Content type ‘application/x-gzip’ length 4194093 bytes (4.0 MB)
downloaded 4.0 MB
trying URL ‘http://cloud.r-project.org/src/contrib/brms_2.15.0.tar.gz’
Content type ‘application/x-gzip’ length 4343133 bytes (4.1 MB)
downloaded 4.1 MB
- installing source package ‘units’ …
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.7-1
checking whether the C++ compiler works… yes
checking for C++ compiler default output file name… a.out
checking for suffix of executables…
checking whether we are cross compiling… no
checking for suffix of object files… o
checking whether we are using the GNU C++ compiler… yes
checking whether clang++ -std=gnu++11 accepts -g… yes
checking how to run the C++ preprocessor… clang++ -std=gnu++11 -E
checking for grep that handles long lines and -e… /usr/bin/grep
checking for egrep… /usr/bin/grep -E
checking for ANSI C header files… rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h… yes
checking for sys/stat.h… yes
checking for stdlib.h… yes
checking for string.h… yes
checking for memory.h… yes
checking for strings.h… yes
checking for inttypes.h… yes
checking for stdint.h… yes
checking for unistd.h… yes
checking for stdbool.h that conforms to C99… no
checking for _Bool… no
checking for error_at_line… no
checking for gcc… clang
checking whether we are using the GNU C compiler… yes
checking whether clang accepts -g… yes
checking for clang option to accept ISO C89… none needed
checking for XML_ParserCreate in -lexpat… yes
checking udunits2.h usability… no
checking udunits2.h presence… no
checking for udunits2.h… no
checking udunits2/udunits2.h usability… no
checking udunits2/udunits2.h presence… no
checking for udunits2/udunits2.h… no
checking for ut_read_xml in -ludunits2… no
configure: error: in `/private/tmp/RtmpfhWJXv/R.INSTALL126f4457faa7/units’:
configure: error:
Configuration failed because libudunits2.so was not found. Try installing:
* deb: libudunits2-dev (Debian, Ubuntu, …)
* rpm: udunits2-devel (Fedora, EPEL, …)
* brew: udunits (OSX)
If udunits2 is already installed in a non-standard location, use:
–configure-args=‘–with-udunits2-lib=/usr/local/lib’
if the library was not found, and/or:
–configure-args=‘–with-udunits2-include=/usr/include/udunits2’
if the header was not found, replacing paths with appropriate values.
You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
See `config.log’ for more details
ERROR: configuration failed for package ‘units’
- removing ‘/Users/amylo/Library/R/4.0/library/units’
- installing source package ‘V8’ …
** package ‘V8’ successfully unpacked and MD5 sums checked
** using staged installation
Found C++14 compiler: clang++
Using CXXCPP=clang++ -std=gnu++14 -E
Using PKG_CFLAGS=-I/usr/local/opt/v8/include -I/usr/local/opt/v8/libexec/include
Using PKG_LIBS=-L/usr/local/opt/v8/libexec -lv8 -lv8_libplatform
-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find the libv8 engine library. Try installing: - deb: libv8-dev or libnode-dev (Debian / Ubuntu)
- rpm: v8-devel (Fedora, EPEL)
- brew: v8 (OSX)
- csw: libv8_dev (Solaris)
Alternatively, on Linux (x86_64) or MacOS you can set environment variable:
DOWNLOAD_STATIC_LIBV8=1
to automatically download a static version of libv8.
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars=‘INCLUDE_DIR=… LIB_DIR=…’
---------------------------[ ERROR MESSAGE ]----------------------------
:1:10: fatal error: ‘v8.h’ file not found
#include <v8.h>
^~~~~~
1 error generated.
ERROR: configuration failed for package ‘V8’
- removing ‘/Users/amylo/Library/R/4.0/library/V8’
- installing source package ‘gsl’ …
** package ‘gsl’ successfully unpacked and MD5 sums checked
** using staged installation
checking for gsl-config… no
configure: error: gsl-config not found, is GSL installed?
ERROR: configuration failed for package ‘gsl’ - removing ‘/Users/amylo/Library/R/4.0/library/gsl’
ERROR: dependency ‘units’ is not available for package ‘sf’ - removing ‘/Users/amylo/Library/R/4.0/library/sf’
ERROR: dependency ‘V8’ is not available for package ‘rstan’ - removing ‘/Users/amylo/Library/R/4.0/library/rstan’
ERROR: dependency ‘gsl’ is not available for package ‘rtdists’ - removing ‘/Users/amylo/Library/R/4.0/library/rtdists’
ERROR: dependency ‘rstan’ is not available for package ‘shinystan’ - removing ‘/Users/amylo/Library/R/4.0/library/shinystan’
ERROR: dependency ‘sf’ is not available for package ‘spdep’ - removing ‘/Users/amylo/Library/R/4.0/library/spdep’
ERROR: dependencies ‘rstan’, ‘shinystan’ are not available for package ‘brms’ - removing ‘/Users/amylo/Library/R/4.0/library/brms’
The downloaded source packages are in
‘/private/tmp/RtmpWH5nFp/downloaded_packages’
++ Note: @ 15:36:30
This package has been installed on the computer: brms
Warning messages:
1: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘units’ had non-zero exit status
2: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘V8’ had non-zero exit status
3: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘gsl’ had non-zero exit status
4: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘sf’ had non-zero exit status
5: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘rstan’ had non-zero exit status
6: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘rtdists’ had non-zero exit status
7: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘shinystan’ had non-zero exit status
8: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘spdep’ had non-zero exit status
9: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘brms’ had non-zero exit status