Hi there,
I checked for AFNI updates and a message appeared indicating that I did not have the relevant R packages installed (I had everything previously). I ran "rPkgsInstall -pkgs ALL" and it seems like it could not be installed properly. I was wondering whether you have any solutions to these errors am receiving?
Thank you,
Tamara
TERMINAL OUTPUT
ttavare@MitchellLabImage2:~$ rPkgsInstall -pkgs ALL
Installing package into ‘/home/ttavare/R’
(as ‘lib’ is unspecified)
Warning: dependency ‘cmdstanr’ is not available
also installing the dependencies ‘igraph’, ‘StanHeaders’, ‘RcppParallel’, ‘threejs’, ‘gsl’, ‘sf’, ‘rstan’, ‘rstantools’, ‘shinystan’, ‘projpred’, ‘rtdists’, ‘spdep’
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 2715500 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 1402572 bytes (1.3 MB)
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downloaded 1.3 MB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 1967752 bytes (1.9 MB)
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downloaded 1.9 MB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 866293 bytes (845 KB)
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downloaded 845 KB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 213803 bytes (208 KB)
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downloaded 208 KB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 3645982 bytes (3.5 MB)
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downloaded 3.5 MB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 1152008 bytes (1.1 MB)
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downloaded 1.1 MB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 91668 bytes (89 KB)
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downloaded 89 KB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 2400413 bytes (2.3 MB)
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downloaded 2.3 MB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 175415 bytes (171 KB)
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downloaded 171 KB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 867210 bytes (846 KB)
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downloaded 846 KB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 4281099 bytes (4.1 MB)
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downloaded 4.1 MB
trying URL '[
cloud.r-project.org];
Content type 'application/x-gzip' length 4954887 bytes (4.7 MB)
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downloaded 4.7 MB
ERROR: failed to lock directory ‘/home/ttavare/R’ for modifying
Try removing ‘/home/ttavare/R/00LOCK-igraph’
* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** using staged installation
** preparing to configure package 'RcppParallel' ...
*** configured file: 'src/Makevars.in' => 'src/Makevars'
** finished configure for package 'RcppParallel'
** libs
(tbb) Building TBB using bundled sources ...
make[1]: Entering directory '/tmp/RtmphUKw5D/R.INSTALL639c5dd5d197/RcppParallel/src/tbb/src'
../build/common.inc:74: *** "" is not supported. Add build/.inc file with os-specific settings . Stop.
make[1]: Leaving directory '/tmp/RtmphUKw5D/R.INSTALL639c5dd5d197/RcppParallel/src/tbb/src'
make: *** [Makevars:152: tbb] Error 2
ERROR: compilation failed for package ‘RcppParallel’
* removing ‘/home/ttavare/R/RcppParallel’
* 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 ‘/home/ttavare/R/gsl’
* installing *source* package ‘sf’ ...
** package ‘sf’ successfully unpacked and MD5 sums checked
** using staged installation
configure: CC: gcc -std=gnu99
configure: CXX: g++ -std=gnu++11
checking for gdal-config... no
no
configure: error: gdal-config not found or not executable.
ERROR: configuration failed for package ‘sf’
* removing ‘/home/ttavare/R/sf’
ERROR: dependency ‘RcppParallel’ is not available for package ‘StanHeaders’
* removing ‘/home/ttavare/R/StanHeaders’
ERROR: dependency ‘igraph’ is not available for package ‘threejs’
* removing ‘/home/ttavare/R/threejs’
ERROR: dependency ‘RcppParallel’ is not available for package ‘rstantools’
* removing ‘/home/ttavare/R/rstantools’
ERROR: dependency ‘gsl’ is not available for package ‘rtdists’
* removing ‘/home/ttavare/R/rtdists’
ERROR: dependency ‘sf’ is not available for package ‘spdep’
* removing ‘/home/ttavare/R/spdep’
ERROR: dependencies ‘StanHeaders’, ‘RcppParallel’ are not available for package ‘rstan’
* removing ‘/home/ttavare/R/rstan’
ERROR: dependency ‘rstantools’ is not available for package ‘projpred’
* removing ‘/home/ttavare/R/projpred’
ERROR: dependencies ‘rstan’, ‘threejs’ are not available for package ‘shinystan’
* removing ‘/home/ttavare/R/shinystan’
ERROR: dependencies ‘rstan’, ‘rstantools’, ‘shinystan’, ‘projpred’ are not available for package ‘brms’
* removing ‘/home/ttavare/R/brms’
The downloaded source packages are in
‘/tmp/RtmpRiNTN4/downloaded_packages’
++ Note: @ 14:55:40
This package has been installed on the computer: brms
There were 13 warnings (use warnings() to see them)
ttavare@MitchellLabImage2:~$
