Hi all,
As a fresh AFNi-install under Windows Subsystem for Linux (WSL), I have some problems during installing R packages needed for AFNI programs. see below.
I have read some related topics on the board and tried solutions highly recommended, but still failed.
I will appreciate it if anyone could give me some help.
input: rPkgsInstall -pkgs ALL
output:
Installing package into ‘/home/xiaodong0203/R’
(as ‘lib’ is unspecified)
also installing the dependencies ‘ps’, ‘processx’, ‘callr’, ‘units’, ‘pkgbuild’, ‘pkgload’, ‘sf’, ‘rstan’, ‘shinystan’, ‘testthat’, ‘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_3.3.2.tar.gz’
Content type ‘application/x-gzip’ length 94404 bytes (92 KB)
downloaded 92 KB
trying URL ‘http://cran.us.r-project.org/src/contrib/units_0.6-5.tar.gz’
Content type ‘application/x-gzip’ length 959970 bytes (937 KB)
downloaded 937 KB
trying URL ‘http://cran.us.r-project.org/src/contrib/pkgbuild_1.0.6.tar.gz’
Content type ‘application/x-gzip’ length 29322 bytes (28 KB)
downloaded 28 KB
trying URL ‘http://cran.us.r-project.org/src/contrib/pkgload_1.0.2.tar.gz’
Content type ‘application/x-gzip’ length 55605 bytes (54 KB)
downloaded 54 KB
trying URL ‘http://cran.us.r-project.org/src/contrib/sf_0.8-0.tar.gz’
Content type ‘application/x-gzip’ length 8607770 bytes (8.2 MB)
downloaded 8.2 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/testthat_2.3.0.tar.gz’
Content type ‘application/x-gzip’ length 247381 bytes (241 KB)
downloaded 241 KB
trying URL ‘http://cran.us.r-project.org/src/contrib/spdep_1.1-3.tar.gz’
Content type ‘application/x-gzip’ length 1230873 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
ERROR: failed to lock directory ‘/home/xiaodong0203/R’ for modifying
Try removing ‘/home/xiaodong0203/R/00LOCK-ps’
- 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/RtmpDUjGMf/R.INSTALL36db5e661cf9/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/xiaodong0203/R/units’
ERROR: dependency ‘ps’ is not available for package ‘processx’ - removing ‘/home/xiaodong0203/R/processx’
ERROR: dependency ‘units’ is not available for package ‘sf’ - removing ‘/home/xiaodong0203/R/sf’
ERROR: dependency ‘processx’ is not available for package ‘callr’ - removing ‘/home/xiaodong0203/R/callr’
ERROR: dependency ‘sf’ is not available for package ‘spdep’ - removing ‘/home/xiaodong0203/R/spdep’
ERROR: dependency ‘callr’ is not available for package ‘pkgbuild’ - removing ‘/home/xiaodong0203/R/pkgbuild’
ERROR: dependency ‘pkgbuild’ is not available for package ‘pkgload’ - removing ‘/home/xiaodong0203/R/pkgload’
ERROR: dependency ‘pkgbuild’ is not available for package ‘rstan’ - removing ‘/home/xiaodong0203/R/rstan’
ERROR: dependency ‘rstan’ is not available for package ‘shinystan’ - removing ‘/home/xiaodong0203/R/shinystan’
ERROR: dependency ‘pkgload’ is not available for package ‘testthat’ - removing ‘/home/xiaodong0203/R/testthat’
ERROR: dependencies ‘rstan’, ‘shinystan’ are not available for package ‘brms’ - removing ‘/home/xiaodong0203/R/brms’
The downloaded source packages are in
‘/tmp/RtmpPP52A9/downloaded_packages’
++ Note: @ 20:08:44
This package has been installed on the computer: brms
There were 12 warnings (use warnings() to see them)
Many thanks in advance.
XD