Dear AFNI oracles,
I have been trying to install AFNI on a ubuntu22.04 computer , and still have some errors I don't manage to overcome.
When I try rPkgsInstall. there are sth wrong with:
In file included from gzipdatasource.cpp:1:
gzipdatasource.h:4:10: fatal error: zlib.h: No such file or directory
4 | #include <zlib.h>
.
.
.
Warning messages (with all Pkgs depended):
In install.packages(pkgs_miss, dep = NA, repos = site) :
This is the output of afni_system_check:
-------------------------------- general ---------------------------------
architecture: 64bit ELF
cpu type: x86_64
system: Linux
release: 6.2.0-32-generic
version: #32~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Fri Aug 18 10:40:13 UTC 2
distribution: Ubuntu 22.04.3 LTS
number of CPUs: 20
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/xiaoyu/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Sep 15 2023
: AFNI_23.2.10 'Marcus Didius Severus Julianus'
AFNI_version.txt : AFNI_23.2.10, linux_ubuntu_16_64, Sep 15 2023, official
which python : /home/xiaoyu/fsl/bin/python
python version : 3.11.5
which R : /opt/R/4.3.1/bin/R
R version : R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
instances of various programs found in PATH:
afni : 1 (/home/xiaoyu/abin/afni)
R : 2
/opt/R/4.3.1/bin/R
/usr/bin/R
python : 2
/home/xiaoyu/fsl/bin/python3.11
/usr/bin/python3.10
python2 : 0
python3 : 2
/home/xiaoyu/fsl/bin/python3.11
/usr/bin/python3.10
** have python3 but not python2
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
uber_subject.py : success
3dMVM : success
------------------------ dependent program tests -------------------------
checking for dependent programs...
which tcsh : /usr/bin/tcsh
which Xvfb : /usr/bin/Xvfb
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: brms!
R RHOME : /opt/R/4.3.1/lib/R
------------------------------ python libs -------------------------------
++ module loaded: matplotlib.pyplot
module file : /home/xiaoyu/fsl/lib/python3.11/site-packages/matplotlib/pyplot.py
matplotlib version : 3.7.2
-------------------------------- env vars --------------------------------
PATH = /opt/R/4.3.1/bin:/home/xiaoyu/fsl/bin:/home/xiaoyu/fsl/share/fsl/bin:/usr/local/freesurfer/bin:/usr/local/freesurfer/fsfast/bin:/usr/local/freesurfer/tktools:/home/xiaoyu/fsl/bin:/home/xiaoyu/fsl/share/fsl/bin:/usr/local/freesurfer/mni/bin:/home/xiaoyu/fsl/share/fsl/bin:/home/xiaoyu/fsl/share/fsl/bin:/home/xiaoyu/.local/bin:/home/xiaoyu/download/software/build/bin/:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/xiaoyu/abin
PYTHONPATH =
R_LIBS = /home/xiaoyu/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
----------------------------- eval dot files -----------------------------
----------- AFNI $HOME files -----------
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
--------- shell startup files ----------
-- good: .tcshrc seems to contain 'source .cshrc'
-- considered operations: path, flatdir, apsearch
(not on a mac, should skip flatdir)
-- note: followers should not need edits, so edit flags should be 0
(have 1 follower(s), which can be ignored)
dot file test : want 1 modifications across 3 files:
file path flatdir apsearch follower
--------------- ---- ------- -------- --------
.cshrc 0 0 1 0
.tcshrc 0 0 0 1
.bashrc 0 0 0 0
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...3 [rickr]: renamed GroupAna_cases scripts and output
data dir : found AFNI_demos under $HOME
top history: ...ct 2020 [taylorp]: updated scripts under FATCAT_DEMO
data dir : found suma_demo under $HOME
top history: ...s_New/data/Build_tmp on Mon Mar 4 11:56:45 EST 2013
data dir : found afni_handouts under $HOME
atlas : found TT_N27+tlrc under /home/xiaoyu/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.4.10 (amd64)
have Ubuntu system: Ubuntu 22.04.3 LTS
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Sep 15 2023
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* missing R packages (see rPkgsInstall)
* dot file test : want 1 modifications across 3 files:
Thanks for the help!
Xiaoyu