3dLME error: "Error in xinit : object 'xinit' not found

AFNI Message Board
1

Hi all,

Attempting to run a 3dLME on a within subjects/repeated measures design (3 diet conditions). We have a max of 20 subjects but some folks are missing data for certain conditions. Interested in main effect of diet condition.

Our 3dLME set up seems to be working okay (we get the contingency table output in terminal), but execution halts shortly after due to an error (“Error in xinit : object ‘xinit’ not found”). Please see output below.

We created a /.Rprofile with 'xinit = “NA” ’ as suggested in this post to no avail, unfortunately.

Any insight would be greatly appreciated!

updating R_LD_LIBRARY_PATH …
Installing package into ‘/Users/darceyvl/Library/R/3.6/library’
(as ‘lib’ is unspecified)
Warning: unable to access index for repository http://watson.nci.nih.gov/cran_mirror/src/contrib:
cannot open URL ‘http://watson.nci.nih.gov/cran_mirror/src/contrib/PACKAGES’
Warning: unable to access index for repository http://watson.nci.nih.gov/cran_mirror/bin/macosx/el-capitan/contrib/3.6:
cannot open URL ‘http://watson.nci.nih.gov/cran_mirror/bin/macosx/el-capitan/contrib/3.6/PACKAGES’
Loading required package: nlme
Package nlme loaded successfully!

Loading required package: phia
Warning messages:
1: package ‘phia’ is not available (for R version 3.6.3)
2: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘phia’

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
20 subjects : s307 s309 s321 s323 s324 s325 s326 s327 s328 s329 s330 s331 s332 s333 s334 s335 s338 s339 s340 s342
54 response values
3 levels for factor diet : baseline lowcarb lowfat
6 post hoc tests

Contingency tables of subject distributions among the categorical variables:

Tabulation of subjects against all categorical variables

Subj vs diet:
      
       baseline lowcarb lowfat
  s307        1       1      1
  s309        1       1      1
  s321        1       1      1
  s323        1       1      1
  s324        1       0      1
  s325        1       1      0
  s326        1       1      1
  s327        1       1      1
  s328        1       1      1
  s329        1       1      1
  s330        1       1      1
  s331        1       1      1
  s332        1       1      0
  s333        1       0      0
  s334        1       1      1
  s335        1       1      1
  s338        1       1      1
  s339        1       1      1
  s340        1       0      1
  s342        1       1      1
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

Reading input files: Done!


Range of input data: [-3.906, 6.055]

If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.

Error in xinit : object 'xinit' not found
Execution halted
2

package ‘phia’ is not available

You need to install the R package ‘phia’.

3

Thanks Gang. I installed ‘phia’ (actually, ran rPkgsInstall -pkgs ALL), but now a new error looking for package ‘data.table’. I did some digging but am not clear on how to fix. Thanks very much for any input!

updating R_LD_LIBRARY_PATH …
Loading required package: nlme
Package nlme loaded successfully!

Loading required package: phia
Loading required package: car
Loading required package: carData
Error: package or namespace load failed for ‘car’ in loadNamespace(j ← i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
there is no package called ‘data.table’
Failed with error: ‘package ‘car’ could not be loaded’

++++++++++++++++++++++++++++++++++++++++++++++++++++
***** Summary information of data structure *****
20 subjects : s307 s309 s321 s323 s324 s325 s326 s327 s328 s329 s330 s331 s332 s333 s334 s335 s338 s339 s340 s342
54 response values
3 levels for factor diet : baseline lowcarb lowfat
6 post hoc tests

Contingency tables of subject distributions among the categorical variables:

Tabulation of subjects against all categorical variables

Subj vs diet:
      
       baseline lowcarb lowfat
  s307        1       1      1
  s309        1       1      1
  s321        1       1      1
  s323        1       1      1
  s324        1       0      1
  s325        1       1      0
  s326        1       1      1
  s327        1       1      1
  s328        1       1      1
  s329        1       1      1
  s330        1       1      1
  s331        1       1      1
  s332        1       1      0
  s333        1       0      0
  s334        1       1      1
  s335        1       1      1
  s338        1       1      1
  s339        1       1      1
  s340        1       0      1
  s342        1       1      1
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now...

Reading input files: Done!


Range of input data: [-3.906, 6.055]

If the program hangs here for more than, for example, half an hour,
kill the process because the model specification or the GLT coding
is likely inappropriate.

Error in xinit : object 'xinit' not found
Execution halted
4

If you’re on a Mac, there seems to have some issue with the most recent version (v1.13.0) of data.table:

https://rdrr.io/github/Rdatatable/data.table/f/NEWS.md

To get around the problem (before the package maintainer fixes the problem in the next version release), install an older version of data.table:

  1. Download the older version from here to a temporal directory:
    https://cran.r-project.org/bin/macosx/el-capitan/contrib/3.6/data.table_1.12.8.tgz

  2. At the terminal, execute the following command:
    R CMD install data.table_1.12.8.tgz

  3. Try your 3dLME script and see if it works.