Hello,
I’m having some trouble installing R packages for AFNI. I’m running Ubuntu in a terminal in Windows 10. I’m also a beginner to both AFNI and Unix/Linux.
Here is the output for rPkgsInstall -pkgs ALL
Installing package into ‘/home/patreyes/R’
(as ‘lib’ is unspecified)
also installing the dependencies ‘ps’, ‘processx’, ‘callr’, ‘units’, ‘pkgbuild’, ‘sf’, ‘rstan’, ‘shinystan’, ‘spdep’
trying URL 'http://cran.us.r-project.org/src/contrib/ps_1.3.0.tar.gz'
Content type 'application/x-gzip' length 261887 bytes (255 KB)
==================================================
downloaded 255 KB
trying URL 'http://cran.us.r-project.org/src/contrib/processx_3.4.1.tar.gz'
Content type 'application/x-gzip' length 123430 bytes (120 KB)
==================================================
downloaded 120 KB
trying URL 'http://cran.us.r-project.org/src/contrib/callr_3.3.1.tar.gz'
Content type 'application/x-gzip' length 94264 bytes (92 KB)
==================================================
downloaded 92 KB
trying URL 'http://cran.us.r-project.org/src/contrib/units_0.6-4.tar.gz'
Content type 'application/x-gzip' length 959885 bytes (937 KB)
==================================================
downloaded 937 KB
trying URL 'http://cran.us.r-project.org/src/contrib/pkgbuild_1.0.5.tar.gz'
Content type 'application/x-gzip' length 29022 bytes (28 KB)
==================================================
downloaded 28 KB
trying URL 'http://cran.us.r-project.org/src/contrib/sf_0.7-7.tar.gz'
Content type 'application/x-gzip' length 8441790 bytes (8.1 MB)
==================================================
downloaded 8.1 MB
trying URL 'http://cran.us.r-project.org/src/contrib/rstan_2.19.2.tar.gz'
Content type 'application/x-gzip' length 909934 bytes (888 KB)
==================================================
downloaded 888 KB
trying URL 'http://cran.us.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://cran.us.r-project.org/src/contrib/spdep_1.1-2.tar.gz'
Content type 'application/x-gzip' length 1227625 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'http://cran.us.r-project.org/src/contrib/brms_2.10.0.tar.gz'
Content type 'application/x-gzip' length 4339824 bytes (4.1 MB)
==================================================
downloaded 4.1 MB
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall px.c -o px
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-common.c -o api-common.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c common.c -o common.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c extra.c -o extra.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dummy.c -o dummy.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c posix.c -o posix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-posix.c -o api-posix.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c linux.c -o linux.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-uuRxut/r-base-3.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-linux.c -o api-linux.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ps.so init.o api-common.o common.o extra.o dummy.o posix.o api-posix.o linux.o api-linux.o -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /home/patreyes/R/00LOCK-ps/00new/ps
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
mv: cannot move '/home/patreyes/R/00LOCK-ps/00new/ps' to '/home/patreyes/R/ps': Permission denied
ERROR: moving to final location failed
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.6-4
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 g++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -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 for stdbool.h that conforms to C99... no
checking for _Bool... no
checking for error_at_line... yes
checking for gcc... gcc -std=gnu99
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 for XML_ParserCreate in -lexpat... no
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 `/tmp/RtmpCuW9ch/R.INSTALL19017f4c9704/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 ‘/home/patreyes/R/units’
ERROR: dependency ‘ps’ is not available for package ‘processx’
* removing ‘/home/patreyes/R/processx’
ERROR: dependency ‘units’ is not available for package ‘sf’
* removing ‘/home/patreyes/R/sf’
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/home/patreyes/R/callr’
ERROR: dependency ‘sf’ is not available for package ‘spdep’
* removing ‘/home/patreyes/R/spdep’
ERROR: dependency ‘callr’ is not available for package ‘pkgbuild’
* removing ‘/home/patreyes/R/pkgbuild’
ERROR: dependency ‘pkgbuild’ is not available for package ‘rstan’
* removing ‘/home/patreyes/R/rstan’
ERROR: dependency ‘rstan’ is not available for package ‘shinystan’
* removing ‘/home/patreyes/R/shinystan’
ERROR: dependencies ‘rstan’, ‘shinystan’ are not available for package ‘brms’
* removing ‘/home/patreyes/R/brms’
The downloaded source packages are in
‘/tmp/RtmpUUGqap/downloaded_packages’
++ Note: @ 15:49:41
This package has been installed on the computer: brms
Warning messages:
1: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘ps’ had non-zero exit status
2: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘units’ had non-zero exit status
3: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘processx’ 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 ‘callr’ had non-zero exit status
6: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘spdep’ had non-zero exit status
7: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘pkgbuild’ had non-zero exit status
8: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘rstan’ had non-zero exit status
9: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘shinystan’ had non-zero exit status
10: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘brms’ had non-zero exit status
And here is the output for: afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 4.4.0-18362-Microsoft
version: #1-Microsoft Mon Mar 18 12:02:00 PST 2019
distribution: Ubuntu 18.04 bionic
number of CPUs: 8
apparent login shell: tcsh
shell RC file: .cshrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/patreyes/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Sep 6 2019
: AFNI_19.2.23 'Claudius'
AFNI_version.txt : AFNI_19.2.23, linux_ubuntu_16_64, Sep 06 2019
which python : /usr/bin/python
python version : 2.7.15+
which R : /usr/bin/R
R version : R version 3.6.1 (2019-07-05) -- "Action of the Toes"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/patreyes/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.6)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : success
uber_subject.py : success
3dAllineate : success
3dRSFC : success
SurfMesh : success
3dClustSim : success
3dMVM : success
checking for R packages...
rPkgsInstall -pkgs ALL -check : FAILURE
oo Warning:
These packages are not installed on the computer: brms!
R RHOME : /usr/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib/python2.7/dist-packages/PyQt4/__init__.pyc
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/mnt/c/WINDOWS/system32:/mnt/c/WINDOWS:/mnt/c/WINDOWS/System32/Wbem:/mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0/:/mnt/c/WINDOWS/System32/OpenSSH/:/mnt/c/Users/reyes/AppData/Local/Microsoft/WindowsApps:/home/patreyes/abin
PYTHONPATH =
R_LIBS = /home/patreyes/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : found AFNI_data6 under $HOME
top history: ...2019 [ptaylor]: updated FT_analysis/results.QC_FT.05
data dir : found AFNI_demos under $HOME
top history: ...ay 2019 [rickr]: AFNI_pamenc updates to global_*.txt
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/patreyes/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 1.6.11 (amd64)
have Ubuntu system: Ubuntu 18.04 bionic
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Sep 6 2019
========================= summary, please fix: =========================
* missing R packages (see rPkgsInstall)
Please let me know if I’ve done something wrong or if I’ve overlooked something. Again, I’m a beginner (this is me prepping for Bootcamp this year)
With Thanks and Sincerely,
P. Reyes