Hello helpful people,
I am trying to install AFNI for the first time in my life. On Windows/WSL/Ubuntu
I followed instructions at https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_windows10.html faithfully (I think), but
========================= summary, please fix: =========================
- missing R packages (see rPkgsInstall)
checking for R packages…
rPkgsInstall -pkgs ALL -check : FAILURE
These packages are not installed on the computer: afex!
These packages are not installed on the computer: phia!
These packages are not installed on the computer: brms!
I tried to re-run rPkgsInstall -pkgs ALL just in case, but it did not solve the issue
(Also, I have no linux/unix experience whatsoever, so please be patient…)
I tried installing libcurl4-openssl-dev as suggested by isospin in the “brms not installed” thread.
This fixed the afex and phia problem, but brms is still reported not installed.
It looks to me that PKI fails to install due to lack of openssl (even though I did sudo apt-get install libcurl4-openssl-dev) and that leads to brms not installed through a chain of dependencies
Any idea how to fix this?
Here us what rPkgsInstall -pkgs ALL returned
- installing source package ‘PKI’ …
** package ‘PKI’ successfully unpacked and MD5 sums checked
checking for gcc… gcc -std=gnu99
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 gcc -std=gnu99 accepts -g… yes
checking for gcc -std=gnu99 option to accept ISO C89… none needed
checking how to run the C preprocessor… gcc -std=gnu99 -E
checking for grep that handles long lines and -e… /bin/grep
checking for egrep… /bin/grep -E
checking for ANSI C header files… 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 openssl/ssl.h usability… no
checking openssl/ssl.h presence… no
checking for openssl/ssl.h… no
checking openssl/rsa.h usability… no
checking openssl/rsa.h presence… no
checking for openssl/rsa.h… no
configure: error: Failed to find usable crypto library. Please install openssl-dev or equivalent and/or set PKG_LIBS if not in default location.
ERROR: configuration failed for package ‘PKI’
- removing ‘/home/pawel/R/PKI’
ERROR: dependency ‘PKI’ is not available for package ‘rsconnect’
- removing ‘/home/pawel/R/rsconnect’
ERROR: dependency ‘rsconnect’ is not available for package ‘shinystan’
- removing ‘/home/pawel/R/shinystan’
ERROR: dependency ‘shinystan’ is not available for package ‘brms’
- removing ‘/home/pawel/R/brms’
From the sound of it you may need to install openssl and openssl-dev. Since you say you are using Ubuntu, you should be able to achieve this with
sudo apt-get install openssl openssl-dev
Note that openssl-dev and libcurl4-openssl-dev are not the same thing. the former is the development support part (e.g., the header files) of the library that provides SSL support. The latter iis the pat of the libcurl4 that provides developmental support for SSL in libcurl4. (Libcurl is the library behing the curl program). I confess, though, that I’m surprised that libcurl4-openssl-dev doesn’t automatically pull in openssl-dev.
I’ve not got an Ubuntu machine on which to try this out so bear that in mind when trying this.
Thank you. This did not help though, I got:
E: Unable to locate package openssl-dev
But someone else recommended
sudo apt-get install libssl-dev
and after that, and reinstallation of R, AFNI installation check return a yay!