errors on R packages (e.g., afex, phia) installation for 3dLME

AFNI Message Board
1

Hello,
I am interested in running 3dLME to analyze our longitudinal fMRI data.
As recommended, I have installed R (3.6.0), but got several warnings/errors when I tried to install afex and phia packages.
I am wondering whether I need a higer version of R or any other system updates.
Any suggestions and thoughts would be very helpful.
Thank you!

Here are output from running “afni_system_check.py” and warnings/errors of afex/phia packages installation.

***afni_system_check.py -check_all ***

-------------------------------- general ---------------------------------
architecture: 64bit ELF
system: Linux
release: 2.6.32-642.el6.x86_64
version: #1 SMP Wed Apr 13 00:51:26 EDT 2016
distribution: Red Hat Enterprise Linux Server 6.8 Santiago
number of CPUs: 28
apparent login shell: bash
shell RC file: .bashrc (exists)

--------------------- AFNI and related program tests ---------------------
which afni : /APP/afni/afni
afni version : Precompiled binary linux_openmp_64: Oct 2 2020
: AFNI_20.3.00 ‘Vespasian’
AFNI_version.txt : AFNI_20.3.00, linux_openmp_64, Oct 02 2020
which python : /usr/bin/python
python version : 2.6.6
which R : /usr/bin/R
R version : R version 3.6.0 (2019-04-26) – “Planting of a Tree”
which tcsh : /bin/tcsh

instances of various programs found in PATH:
afni : 1 (/APP/afni/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python)
python2 : 1 (/usr/bin/python)
python3 : 0

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: afex!
    These packages are not installed on the computer: phia!
    These packages are not installed on the computer: lmerTest!
    These packages are not installed on the computer: brms!

R RHOME : /usr/lib64/R

checking for $HOME files…
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found

------------------------------ python libs -------------------------------
++ module loaded: PyQt4
module file : /usr/lib64/python2.6/site-packages/PyQt4/init.pyc

/usr/lib64/python2.6/site-packages/gtk-2.0/gtk/init.py:122: RuntimeWarning: PyOS_InputHook is not available for interactive use of PyGTK
set_interactive(1)
++ module loaded: matplotlib.pyplot
module file : /usr/lib64/python2.6/site-packages/matplotlib/pyplot.pyc

*** R afex packages warnings/or errors ***

  • installing source package ‘farver’ …
    ** package ‘farver’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    Error in .shlib_internal(args) :
    C++11 standard requested but CXX11 is not defined
  • removing ‘/usr/lib64/R/library/farver’
  • installing source package ‘RcppArmadillo’ …
    ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
    ** using staged installation
    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++ -m64 -std=gnu++98 accepts -g… yes
    checking how to run the C++ preprocessor… g++ -m64 -std=gnu++98 -E
    checking whether we are using the GNU C++ compiler… (cached) yes
    checking whether g++ -m64 -std=gnu++98 accepts -g… (cached) yes
    checking whether we have a suitable tempdir… /tmp
    checking whether R CMD SHLIB can already compile programs using OpenMP… yes
    checking LAPACK_LIBS… R-supplied partial LAPACK found
    configure: WARNING: Some complex-valued LAPACK functions may not be available
    configure: creating ./config.status
    config.status: creating inst/include/RcppArmadilloConfigGenerated.h
    config.status: creating src/Makevars
    ** libs
    Error in .shlib_internal(args) :
    C++11 standard requested but CXX11 is not defined
  • removing ‘/usr/lib64/R/library/RcppArmadillo’
  • installing source package ‘digest’ …
    ** package ‘digest’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    Error in .shlib_internal(args) :
    C++11 standard requested but CXX11 is not defined
  • removing ‘/usr/lib64/R/library/digest’
  • installing source package ‘data.table’ …
    ** package ‘data.table’ successfully unpacked and MD5 sums checked
    ** using staged installation
    gcc -m64 -std=gnu99 4.4.7
    zlib 1.2.3 is available ok
    OpenMP supported
    ** libs
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c assign.c -o assign.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c between.c -o between.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c bmerge.c -o bmerge.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c chmatch.c -o chmatch.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c cj.c -o cj.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c coalesce.c -o coalesce.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c dogroups.c -o dogroups.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c fastmean.c -o fastmean.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c fcast.c -o fcast.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c fifelse.c -o fifelse.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c fmelt.c -o fmelt.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c forder.c -o forder.o
    forder.c: In function ‘range_str’:
    forder.c:299: error: expected end of line before ‘update’
    make: *** [forder.o] Error 1
    ERROR: compilation failed for package ‘data.table’
  • removing ‘/usr/lib64/R/library/data.table’
    ERROR: dependency ‘digest’ is not available for package ‘testthat’
  • removing ‘/usr/lib64/R/library/testthat’
    ERROR: dependency ‘digest’ is not available for package ‘vctrs’
  • removing ‘/usr/lib64/R/library/vctrs’
    ERROR: dependency ‘farver’ is not available for package ‘scales’
  • removing ‘/usr/lib64/R/library/scales’
    ERROR: dependency ‘RcppArmadillo’ is not available for package ‘conquer’
  • removing ‘/usr/lib64/R/library/conquer’
    ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
  • removing ‘/usr/lib64/R/library/pillar’
    ERROR: dependency ‘vctrs’ is not available for package ‘hms’
  • removing ‘/usr/lib64/R/library/hms’
    ERROR: dependency ‘vctrs’ is not available for package ‘tidyselect’
  • removing ‘/usr/lib64/R/library/tidyselect’
    ERROR: dependency ‘testthat’ is not available for package ‘isoband’
  • removing ‘/usr/lib64/R/library/isoband’
    ERROR: dependency ‘conquer’ is not available for package ‘quantreg’
  • removing ‘/usr/lib64/R/library/quantreg’
    ERROR: dependency ‘hms’ is not available for package ‘progress’
  • removing ‘/usr/lib64/R/library/progress’
    ERROR: dependencies ‘pillar’, ‘vctrs’ are not available for package ‘tibble’
  • removing ‘/usr/lib64/R/library/tibble’
    ERROR: dependency ‘tibble’ is not available for package ‘forcats’
  • removing ‘/usr/lib64/R/library/forcats’
    ERROR: dependencies ‘hms’, ‘tibble’ are not available for package ‘readr’
  • removing ‘/usr/lib64/R/library/readr’
    ERROR: dependency ‘tibble’ is not available for package ‘cellranger’
  • removing ‘/usr/lib64/R/library/cellranger’
    ERROR: dependencies ‘digest’, ‘isoband’, ‘scales’, ‘tibble’ are not available for package ‘ggplot2’
  • removing ‘/usr/lib64/R/library/ggplot2’
    ERROR: dependencies ‘forcats’, ‘hms’, ‘readr’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘haven’
  • removing ‘/usr/lib64/R/library/haven’
    ERROR: dependencies ‘cellranger’, ‘tibble’, ‘progress’ are not available for package ‘readxl’
  • removing ‘/usr/lib64/R/library/readxl’
    ERROR: dependency ‘ggplot2’ is not available for package ‘lmerTest’
  • removing ‘/usr/lib64/R/library/lmerTest’
    ERROR: dependencies ‘haven’, ‘data.table’, ‘readxl’, ‘tibble’ are not available for package ‘rio’
  • removing ‘/usr/lib64/R/library/rio’
    ERROR: dependencies ‘quantreg’, ‘rio’ are not available for package ‘car’
  • removing ‘/usr/lib64/R/library/car’
    ERROR: dependencies ‘lmerTest’, ‘car’ are not available for package ‘afex’
  • removing ‘/usr/lib64/R/library/afex’

The downloaded source packages are in
‘/tmp/RtmpeNtr5m/downloaded_packages’
Updating HTML index of packages in ‘.Library’
Making ‘packages.html’ … done
There were 25 warnings (use warnings() to see them)

*** R phia packages warnings/or errors ***

install.packages(“phia”)
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
— Please select a CRAN mirror for use in this session —
also installing the dependencies ‘digest’, ‘RcppArmadillo’, ‘forcats’, ‘hms’, ‘readr’, ‘tidyselect’, ‘vctrs’, ‘cellranger’, ‘progress’, ‘pillar’, ‘conquer’, ‘haven’, ‘data.table’, ‘readxl’, ‘tibble’, ‘quantreg’, ‘rio’, ‘car’

trying URL ‘https://cran.seoul.go.kr/src/contrib/digest_0.6.26.tar.gz’
Content type ‘application/x-gzip’ length 163988 bytes (160 KB)

downloaded 160 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/RcppArmadillo_0.10.1.0.0.tar.gz’
Content type ‘application/x-gzip’ length 1643776 bytes (1.6 MB)

downloaded 1.6 MB

trying URL ‘https://cran.seoul.go.kr/src/contrib/forcats_0.5.0.tar.gz’
Content type ‘application/x-gzip’ length 257126 bytes (251 KB)

downloaded 251 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/hms_0.5.3.tar.gz’
Content type ‘application/x-gzip’ length 134669 bytes (131 KB)

downloaded 131 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/readr_1.4.0.tar.gz’
Content type ‘application/x-gzip’ length 488946 bytes (477 KB)

downloaded 477 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/tidyselect_1.1.0.tar.gz’
Content type ‘application/x-gzip’ length 90842 bytes (88 KB)

downloaded 88 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/vctrs_0.3.4.tar.gz’
Content type ‘application/x-gzip’ length 995078 bytes (971 KB)

downloaded 971 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/cellranger_1.1.0.tar.gz’
Content type ‘application/x-gzip’ length 63857 bytes (62 KB)

downloaded 62 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/progress_1.2.2.tar.gz’
Content type ‘application/x-gzip’ length 29506 bytes (28 KB)

downloaded 28 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/pillar_1.4.6.tar.gz’
Content type ‘application/x-gzip’ length 113884 bytes (111 KB)

downloaded 111 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/conquer_1.0.2.tar.gz’
Content type ‘application/x-gzip’ length 12322 bytes (12 KB)

downloaded 12 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/haven_2.3.1.tar.gz’
Content type ‘application/x-gzip’ length 277509 bytes (271 KB)

downloaded 271 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/data.table_1.13.2.tar.gz’
Content type ‘application/x-gzip’ length 5282452 bytes (5.0 MB)

downloaded 5.0 MB

trying URL ‘https://cran.seoul.go.kr/src/contrib/readxl_1.3.1.tar.gz’
Content type ‘application/x-gzip’ length 2056165 bytes (2.0 MB)

downloaded 2.0 MB

trying URL ‘https://cran.seoul.go.kr/src/contrib/tibble_3.0.4.tar.gz’
Content type ‘application/x-gzip’ length 255457 bytes (249 KB)

downloaded 249 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/quantreg_5.74.tar.gz’
Content type ‘application/x-gzip’ length 1006486 bytes (982 KB)

downloaded 982 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/rio_0.5.16.tar.gz’
Content type ‘application/x-gzip’ length 420489 bytes (410 KB)

downloaded 410 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/car_3.0-10.tar.gz’
Content type ‘application/x-gzip’ length 501293 bytes (489 KB)

downloaded 489 KB

trying URL ‘https://cran.seoul.go.kr/src/contrib/phia_0.2-1.tar.gz’
Content type ‘application/x-gzip’ length 547339 bytes (534 KB)

downloaded 534 KB

  • installing source package ‘digest’ …
    ** package ‘digest’ successfully unpacked and MD5 sums checked
    ** using staged installation
    ** libs
    Error in .shlib_internal(args) :
    C++11 standard requested but CXX11 is not defined
  • removing ‘/usr/lib64/R/library/digest’
  • installing source package ‘RcppArmadillo’ …
    ** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
    ** using staged installation
    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++ -m64 -std=gnu++98 accepts -g… yes
    checking how to run the C++ preprocessor… g++ -m64 -std=gnu++98 -E
    checking whether we are using the GNU C++ compiler… (cached) yes
    checking whether g++ -m64 -std=gnu++98 accepts -g… (cached) yes
    checking whether we have a suitable tempdir… /tmp
    checking whether R CMD SHLIB can already compile programs using OpenMP… yes
    checking LAPACK_LIBS… R-supplied partial LAPACK found
    configure: WARNING: Some complex-valued LAPACK functions may not be available
    configure: creating ./config.status
    config.status: creating inst/include/RcppArmadilloConfigGenerated.h
    config.status: creating src/Makevars
    ** libs
    Error in .shlib_internal(args) :
    C++11 standard requested but CXX11 is not defined
  • removing ‘/usr/lib64/R/library/RcppArmadillo’
  • installing source package ‘data.table’ …
    ** package ‘data.table’ successfully unpacked and MD5 sums checked
    ** using staged installation
    gcc -m64 -std=gnu99 4.4.7
    zlib 1.2.3 is available ok
    OpenMP supported
    ** libs
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c assign.c -o assign.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c between.c -o between.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c bmerge.c -o bmerge.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c chmatch.c -o chmatch.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c cj.c -o cj.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c coalesce.c -o coalesce.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c dogroups.c -o dogroups.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c fastmean.c -o fastmean.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c fcast.c -o fcast.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c fifelse.c -o fifelse.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c fmelt.c -o fmelt.o
    gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fopenmp -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic -fpic -fPIC -c forder.c -o forder.o
    forder.c: In function ‘range_str’:
    forder.c:299: error: expected end of line before ‘update’
    make: *** [forder.o] Error 1
    ERROR: compilation failed for package ‘data.table’
  • removing ‘/usr/lib64/R/library/data.table’
    ERROR: dependency ‘digest’ is not available for package ‘vctrs’
  • removing ‘/usr/lib64/R/library/vctrs’
    ERROR: dependency ‘RcppArmadillo’ is not available for package ‘conquer’
  • removing ‘/usr/lib64/R/library/conquer’
    ERROR: dependency ‘vctrs’ is not available for package ‘hms’
  • removing ‘/usr/lib64/R/library/hms’
    ERROR: dependency ‘vctrs’ is not available for package ‘tidyselect’
  • removing ‘/usr/lib64/R/library/tidyselect’
    ERROR: dependency ‘vctrs’ is not available for package ‘pillar’
  • removing ‘/usr/lib64/R/library/pillar’
    ERROR: dependency ‘conquer’ is not available for package ‘quantreg’
  • removing ‘/usr/lib64/R/library/quantreg’
    ERROR: dependency ‘hms’ is not available for package ‘progress’
  • removing ‘/usr/lib64/R/library/progress’
    ERROR: dependencies ‘pillar’, ‘vctrs’ are not available for package ‘tibble’
  • removing ‘/usr/lib64/R/library/tibble’
    ERROR: dependency ‘tibble’ is not available for package ‘forcats’
  • removing ‘/usr/lib64/R/library/forcats’
    ERROR: dependencies ‘hms’, ‘tibble’ are not available for package ‘readr’
  • removing ‘/usr/lib64/R/library/readr’
    ERROR: dependency ‘tibble’ is not available for package ‘cellranger’
  • removing ‘/usr/lib64/R/library/cellranger’
    ERROR: dependencies ‘forcats’, ‘hms’, ‘readr’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘haven’
  • removing ‘/usr/lib64/R/library/haven’
    ERROR: dependencies ‘cellranger’, ‘tibble’, ‘progress’ are not available for package ‘readxl’
  • removing ‘/usr/lib64/R/library/readxl’
    ERROR: dependencies ‘haven’, ‘data.table’, ‘readxl’, ‘tibble’ are not available for package ‘rio’
  • removing ‘/usr/lib64/R/library/rio’
    ERROR: dependencies ‘quantreg’, ‘rio’ are not available for package ‘car’
  • removing ‘/usr/lib64/R/library/car’
    ERROR: dependency ‘car’ is not available for package ‘phia’
  • removing ‘/usr/lib64/R/library/phia’

The downloaded source packages are in
‘/tmp/RtmpeNtr5m/downloaded_packages’
Updating HTML index of packages in ‘.Library’
Making ‘packages.html’ … done
There were 19 warnings (use warnings() to see them)

2

C++11 standard requested but CXX11 is not defined

It looks like you have a C++ compiler issue on your Linux system that needs to get resolved. Is your OS (Red Hat 6.8) a little outdated?

3

Hi Gang,
Thanks for your help.
I tried to solve the C++ complier issue but I still have problems with installing R packages.
Thus, our lab have decided to upgrade our OS.
Could you recommend Red Hat version and R version if you have?
I am wondering whether the most recent versions of OS and R would be OK.

Best,
Kyung

4

I do not know of anyone using Red Hat/Cent OS 8 yet (out for a year), but I would expect it to work. The R packages are getting a little difficult to deal with these days, regardless of the OS.

  • rick
5

Dear AFNI experts

I have also a ‘phia’ install problems:

The OS is CentOS Linux release 7.9.2009 (Core)；
The R is R version 3.6.0 (2019-04-26) – “Planting of a Tree”
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-redhat-linux-gnu (64-bit)

[root@localhost abin]# ./rPkgsInstall -pkgs ‘phia’ -update -site ‘http://cloud.r-project.org’
Installing package into ‘/root/R’
(as ‘lib’ is unspecified)
also installing the dependencies ‘curl’, ‘pbkrtest’, ‘rio’, ‘nloptr’, ‘car’, ‘lme4’

trying URL ‘http://cloud.r-project.org/src/contrib/curl_4.3.tar.gz’
Content type ‘application/x-gzip’ length 673779 bytes (657 KB)

downloaded 657 KB

trying URL ‘http://cloud.r-project.org/src/contrib/pbkrtest_0.5.1.tar.gz’
Content type ‘application/x-gzip’ length 246327 bytes (240 KB)

downloaded 240 KB

trying URL ‘http://cloud.r-project.org/src/contrib/rio_0.5.26.tar.gz’
Content type ‘application/x-gzip’ length 384305 bytes (375 KB)

downloaded 375 KB

trying URL ‘http://cloud.r-project.org/src/contrib/nloptr_1.2.2.2.tar.gz’
Content type ‘application/x-gzip’ length 2450931 bytes (2.3 MB)

downloaded 2.3 MB

trying URL ‘http://cloud.r-project.org/src/contrib/car_3.0-10.tar.gz’
Content type ‘application/x-gzip’ length 501293 bytes (489 KB)

downloaded 489 KB

trying URL ‘http://cloud.r-project.org/src/contrib/lme4_1.1-26.tar.gz’
Content type ‘application/x-gzip’ length 3297635 bytes (3.1 MB)

downloaded 3.1 MB

trying URL ‘http://cloud.r-project.org/src/contrib/phia_0.2-1.tar.gz’
Content type ‘application/x-gzip’ length 547339 bytes (534 KB)

downloaded 534 KB

  • installing source package ‘curl’ …
    ** package ‘curl’ successfully unpacked and MD5 sums checked
    ** using staged installation
    Package libcurl was not found in the pkg-config search path.
    Perhaps you should add the directory containing libcurl.pc' to the PKG_CONFIG_PATH environment variable No package 'libcurl' found Package libcurl was not found in the pkg-config search path. Perhaps you should add the directory containing libcurl.pc’
    to the PKG_CONFIG_PATH environment variable
    No package ‘libcurl’ found
    Using PKG_CFLAGS=
    Using PKG_LIBS=-lcurl
    ------------------------- ANTICONF ERROR ---------------------------
    Configuration failed because libcurl was not found. Try installing:
  • deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
  • rpm: libcurl-devel (Fedora, CentOS, RHEL)
  • csw: libcurl_dev (Solaris)
    If libcurl is already installed, check that ‘pkg-config’ is in your
    PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
    is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
    R CMD INSTALL --configure-vars=‘INCLUDE_DIR=… LIB_DIR=…’

ERROR: configuration failed for package ‘curl’

  • removing ‘/root/R/curl’
  • installing source package ‘nloptr’ …
    ** package ‘nloptr’ successfully unpacked and MD5 sums checked
    ** using staged installation
    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++ -m64 -std=gnu++11 accepts -g… yes
    checking how to run the C++ preprocessor… g++ -m64 -std=gnu++11 -E
    checking whether we are using the GNU C++ compiler… (cached) yes
    checking whether g++ -m64 -std=gnu++11 accepts -g… (cached) yes
    checking for pkg-config… yes
    configure: Now testing for NLopt header file.
    checking for grep that handles long lines and -e… /usr/bin/grep
    checking for egrep… /usr/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 nlopt.h usability… no
    checking nlopt.h presence… no
    checking for nlopt.h… no
    configure: Need to configure and build NLopt
    configure: Starting to install library to /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src
    checking for a BSD-compatible install… /usr/bin/install -c
    checking whether build environment is sane… yes
    checking for a thread-safe mkdir -p… /usr/bin/mkdir -p
    checking for gawk… gawk
    checking whether make sets $(MAKE)… yes
    checking whether make supports nested variables… yes
    checking whether to enable maintainer-specific portions of Makefiles… no
    checking for gcc… gcc -m64 -std=gnu99
    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 gcc -m64 -std=gnu99 accepts -g… yes
    checking for gcc -m64 -std=gnu99 option to accept ISO C89… none needed
    checking whether gcc -m64 -std=gnu99 understands -c and -o together… yes
    checking for style of include used by make… GNU
    checking dependency style of gcc -m64 -std=gnu99… gcc3
    checking for gcc -m64 -std=gnu99 option to accept ISO C99… none needed
    checking for gcc -m64 -std=gnu99 option to accept ISO Standard C… (cached) none needed
    checking whether ln -s works… yes
    checking whether make sets $(MAKE)… (cached) yes
    checking build system type… x86_64-unknown-linux-gnu
    checking host system type… x86_64-unknown-linux-gnu
    checking how to print strings… printf
    checking for a sed that does not truncate output… /usr/bin/sed
    checking for grep that handles long lines and -e… /usr/bin/grep
    checking for egrep… /usr/bin/grep -E
    checking for fgrep… /usr/bin/grep -F
    checking for ld used by gcc -m64 -std=gnu99… /usr/bin/ld
    checking if the linker (/usr/bin/ld) is GNU ld… yes
    checking for BSD- or MS-compatible name lister (nm)… /usr/bin/nm -B
    checking the name lister (/usr/bin/nm -B) interface… BSD nm
    checking the maximum length of command line arguments… 1572864
    checking whether the shell understands some XSI constructs… yes
    checking whether the shell understands “+=”… yes
    checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format… func_convert_file_noop
    checking how to convert x86_64-unknown-linux-gnu file names to toolchain format… func_convert_file_noop
    checking for /usr/bin/ld option to reload object files… -r
    checking for objdump… objdump
    checking how to recognize dependent libraries… pass_all
    checking for dlltool… dlltool
    checking how to associate runtime and link libraries… printf %s\n
    checking for archiver @FILE support… no
    checking for strip… strip
    checking for ranlib… ERROR: no information for variable ‘RANLIB’
    checking command to parse /usr/bin/nm -B output from gcc -m64 -std=gnu99 object… ok
    checking for sysroot… no
    checking for mt… no
    checking if : is a manifest tool… no
    checking how to run the C preprocessor… gcc -m64 -std=gnu99 -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 dlfcn.h… yes
    checking for objdir… .libs
    checking if gcc -m64 -std=gnu99 supports -fno-rtti -fno-exceptions… no
    checking for gcc -m64 -std=gnu99 option to produce PIC… -fPIC -DPIC
    checking if gcc -m64 -std=gnu99 PIC flag -fPIC -DPIC works… yes
    checking if gcc -m64 -std=gnu99 static flag -static works… no
    checking if gcc -m64 -std=gnu99 supports -c -o file.o… yes
    checking if gcc -m64 -std=gnu99 supports -c -o file.o… (cached) yes
    checking whether the gcc -m64 -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries… yes
    checking whether -lc should be explicitly linked in… no
    checking dynamic linker characteristics… GNU/Linux ld.so
    checking how to hardcode library paths into programs… immediate
    checking whether stripping libraries is possible… yes
    checking if libtool supports shared libraries… yes
    checking whether to build shared libraries… yes
    checking whether to build static libraries… yes
    checking whether we are using the GNU C++ compiler… yes
    checking whether g++ -m64 -std=gnu++11 accepts -g… yes
    checking dependency style of g++ -m64 -std=gnu++11… gcc3
    checking how to run the C++ preprocessor… g++ -m64 -std=gnu++11 -E
    checking for ld used by g++ -m64 -std=gnu++11… /usr/bin/ld -m elf_x86_64
    checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld… yes
    checking whether the g++ -m64 -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries… yes
    checking for g++ -m64 -std=gnu++11 option to produce PIC… -fPIC -DPIC
    checking if g++ -m64 -std=gnu++11 PIC flag -fPIC -DPIC works… yes
    checking if g++ -m64 -std=gnu++11 static flag -static works… no
    checking if g++ -m64 -std=gnu++11 supports -c -o file.o… yes
    checking if g++ -m64 -std=gnu++11 supports -c -o file.o… (cached) yes
    checking whether the g++ -m64 -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries… yes
    checking dynamic linker characteristics… (cached) GNU/Linux ld.so
    checking how to hardcode library paths into programs… immediate
    checking for ANSI C header files… (cached) yes
    checking whether time.h and sys/time.h may both be included… yes
    checking for unistd.h… (cached) yes
    checking getopt.h usability… yes
    checking getopt.h presence… yes
    checking for getopt.h… yes
    checking for stdint.h… (cached) yes
    checking for an ANSI C-conforming const… yes
    checking for inline… inline
    checking for C thread-local keyword… __thread
    checking size of unsigned int… 4
    checking size of unsigned long… 8
    checking for uint32_t… yes
    checking for sin in -lm… yes
    checking for BSDgettimeofday… no
    checking for gettimeofday… yes
    checking for time… yes
    checking for qsort_r… yes
    checking for getpid… yes
    checking for gettid syscall… yes
    checking for isnan… yes
    checking for isinf… yes
    checking for copysign… yes
    checking for mkoctfile… no
    checking for mex… no
    checking for working HUGE_VAL… ok
    checking that generated files are newer than configure… done
    configure: creating ./config.status
    config.status: creating Makefile
    config.status: creating nlopt.pc
    config.status: creating api/Makefile
    config.status: creating util/Makefile
    config.status: creating octave/Makefile
    config.status: creating direct/Makefile
    config.status: creating cdirect/Makefile
    config.status: creating stogo/Makefile
    config.status: creating praxis/Makefile
    config.status: creating luksan/Makefile
    config.status: creating crs/Makefile
    config.status: creating mlsl/Makefile
    config.status: creating mma/Makefile
    config.status: creating cobyla/Makefile
    config.status: creating newuoa/Makefile
    config.status: creating neldermead/Makefile
    config.status: creating auglag/Makefile
    config.status: creating bobyqa/Makefile
    config.status: creating isres/Makefile
    config.status: creating slsqp/Makefile
    config.status: creating esch/Makefile
    config.status: creating test/Makefile
    config.status: creating swig/Makefile
    config.status: creating swig/nlopt.scm
    config.status: creating config.h
    config.status: executing depfiles commands
    config.status: executing libtool commands
    make all-recursive
    make[1]: Entering directory /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src' Making all in util make[2]: Entering directory /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src/util’
    /bin/sh …/libtool --tag=CC --mode=compile g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT mt19937ar.lo -MD -MP -MF .deps/mt19937ar.Tpo -c -o mt19937ar.lo mt19937ar.c
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT mt19937ar.lo -MD -MP -MF .deps/mt19937ar.Tpo -c mt19937ar.c -fPIC -DPIC -o .libs/mt19937ar.o
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT mt19937ar.lo -MD -MP -MF .deps/mt19937ar.Tpo -c mt19937ar.c -o mt19937ar.o >/dev/null 2>&1
    mv -f .deps/mt19937ar.Tpo .deps/mt19937ar.Plo
    /bin/sh …/libtool --tag=CC --mode=compile g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT sobolseq.lo -MD -MP -MF .deps/sobolseq.Tpo -c -o sobolseq.lo sobolseq.c
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT sobolseq.lo -MD -MP -MF .deps/sobolseq.Tpo -c sobolseq.c -fPIC -DPIC -o .libs/sobolseq.o
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT sobolseq.lo -MD -MP -MF .deps/sobolseq.Tpo -c sobolseq.c -o sobolseq.o >/dev/null 2>&1
    mv -f .deps/sobolseq.Tpo .deps/sobolseq.Plo
    /bin/sh …/libtool --tag=CC --mode=compile g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT timer.lo -MD -MP -MF .deps/timer.Tpo -c -o timer.lo timer.c
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT timer.lo -MD -MP -MF .deps/timer.Tpo -c timer.c -fPIC -DPIC -o .libs/timer.o
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT timer.lo -MD -MP -MF .deps/timer.Tpo -c timer.c -o timer.o >/dev/null 2>&1
    mv -f .deps/timer.Tpo .deps/timer.Plo
    /bin/sh …/libtool --tag=CC --mode=compile g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT stop.lo -MD -MP -MF .deps/stop.Tpo -c -o stop.lo stop.c
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT stop.lo -MD -MP -MF .deps/stop.Tpo -c stop.c -fPIC -DPIC -o .libs/stop.o
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT stop.lo -MD -MP -MF .deps/stop.Tpo -c stop.c -o stop.o >/dev/null 2>&1
    mv -f .deps/stop.Tpo .deps/stop.Plo
    /bin/sh …/libtool --tag=CC --mode=compile g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT redblack.lo -MD -MP -MF .deps/redblack.Tpo -c -o redblack.lo redblack.c
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT redblack.lo -MD -MP -MF .deps/redblack.Tpo -c redblack.c -fPIC -DPIC -o .libs/redblack.o
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT redblack.lo -MD -MP -MF .deps/redblack.Tpo -c redblack.c -o redblack.o >/dev/null 2>&1
    mv -f .deps/redblack.Tpo .deps/redblack.Plo
    /bin/sh …/libtool --tag=CC --mode=compile g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT qsort_r.lo -MD -MP -MF .deps/qsort_r.Tpo -c -o qsort_r.lo qsort_r.c
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT qsort_r.lo -MD -MP -MF .deps/qsort_r.Tpo -c qsort_r.c -fPIC -DPIC -o .libs/qsort_r.o
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT qsort_r.lo -MD -MP -MF .deps/qsort_r.Tpo -c qsort_r.c -o qsort_r.o >/dev/null 2>&1
    mv -f .deps/qsort_r.Tpo .deps/qsort_r.Plo
    /bin/sh …/libtool --tag=CC --mode=compile g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT rescale.lo -MD -MP -MF .deps/rescale.Tpo -c -o rescale.lo rescale.c
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT rescale.lo -MD -MP -MF .deps/rescale.Tpo -c rescale.c -fPIC -DPIC -o .libs/rescale.o
    libtool: compile: g++ -m64 -std=gnu++11 -DHAVE_CONFIG_H -I. -I… -I…/api -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -MT rescale.lo -MD -MP -MF .deps/rescale.Tpo -c rescale.c -o rescale.o >/dev/null 2>&1
    mv -f .deps/rescale.Tpo .deps/rescale.Plo
    /bin/sh …/libtool --tag=CC --mode=link g++ -m64 -std=gnu++11 -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -o libutil.la mt19937ar.lo sobolseq.lo timer.lo stop.lo redblack.lo qsort_r.lo rescale.lo -lm
    libtool: link: ERROR: no information for variable ‘AR’ cru .libs/libutil.a .libs/mt19937ar.o .libs/sobolseq.o .libs/timer.o .libs/stop.o .libs/redblack.o .libs/qsort_r.o .libs/rescale.o
    …/libtool: line 1102: ERROR:: command not found
    make[2]: *** [libutil.la] Error 127
    make[2]: Leaving directory /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src/util' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory /tmp/RtmpHZMqHj/R.INSTALL5ad44606040b1/nloptr/src/nlopt_src’
    make: *** [all] Error 2
    ERROR: configuration failed for package ‘nloptr’
  • removing ‘/root/R/nloptr’
    ERROR: dependency ‘curl’ is not available for package ‘rio’
  • removing ‘/root/R/rio’
    ERROR: dependency ‘nloptr’ is not available for package ‘lme4’
  • removing ‘/root/R/lme4’
    ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
  • removing ‘/root/R/pbkrtest’
    ERROR: dependencies ‘pbkrtest’, ‘rio’, ‘lme4’ are not available for package ‘car’
  • removing ‘/root/R/car’
    ERROR: dependency ‘car’ is not available for package ‘phia’
  • removing ‘/root/R/phia’

The downloaded source packages are in
‘/tmp/RtmpwNBwOB/downloaded_packages’

++ Note: @ 17:21:56
This package has been installed on the computer: phia

++ Note: @ 17:21:57
This package has been updated on the computer:

Warning messages:
1: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘curl’ had non-zero exit status
2: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘nloptr’ had non-zero exit status
3: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘rio’ had non-zero exit status
4: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘lme4’ had non-zero exit status
5: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘pbkrtest’ had non-zero exit status
6: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘car’ had non-zero exit status
7: In install.packages(pkgs_miss, dep = TRUE, repos = site) :
installation of package ‘phia’ had non-zero exit status

6

Not sure if this helps. Try fixing those installation errors one by one. Maybe start with the first one:

ERROR: configuration failed for package ‘nloptr’

Check out this: https://stackoverflow.com/questions/60096357/unable-to-install-r-package-nloptr-r3-6-2-on-ubuntu-16-04-c-compiler-iss

7

Hi Gang
Thanks, Now I have intalled “nlme”, “lme4”, “phia”, “snow” (checking them in the R with installed.packages()).
However, new error comes when trying 3dLME:

Briefly, it is “Error in if (ii < dimx) ii ← ii + 1 else if (jj < dimy) { :
missing value where TRUE/FALSE needed
Execution halted”

The script is "3dLME -prefix Example3 -jobs 2
-ML
-resid Cancha
-qVars “education,age”
-model “CiJiQainHouContrast3+CiJi:QainHou:age:education”
-mask …/newaal_50+tlrc
-ranEff ‘~1’
-SS_type 3
-num_glt 34
-gltLabel 1 anode_sham -gltCode 1 ‘CiJi : 1anode -1sham’
-gltLabel 2 anode_sham_in_after_now -gltCode 2 ‘CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1now’
-gltLabel 3 anode_sham_in_after_notnow -gltCode 3 ‘CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1notnow’
-gltLabel 4 anode_sham_in_after_now_notnow -gltCode 4 ‘CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1now -1notnow’
-gltLabel 5 anode_sham_in_after_now_or_notnow -gltCode 5 'CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1now +1notnow’
-gltLabel 6 after_before_in_anode_now -gltCode 6 ‘CiJi : 1anode QainHou : 1after -1before Contrast3 : 1now’
-gltLabel 7 after_before_in_anode_notnow -gltCode 7 ‘CiJi : 1anode QainHou : 1after -1before Contrast3 : 1notnow’
-gltLabel 8 after_before_in_anode_now_or_notnow -gltCode 8 ‘CiJi : 1anode QainHou : 1after -1before Contrast3 : 1now +1notnow’
-gltLabel 9 CiJi_x_QianHou_now -gltCode 9 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1now’
-gltLabel 10 CiJi_x_QianHou_notnow -gltCode 10 ‘CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1notnow’
-gltLabel 11 CiJi_x_QianHou_now_notnow_3inter -gltCode 11 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1now -1notnow’
-gltLabel 12 CiJi_x_QianHou_now_or_notnow -gltCode 12 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1now +1notnow’
-gltLabel 13 anode_sham_in_after_buyizhi -gltCode 13 'CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1buyizhi’
-gltLabel 14 anode_sham_in_after_yizhi -gltCode 14 'CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1yizhi’
-gltLabel 15 anode_sham_in_after_pmt -gltCode 15 'CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1pmt’
-gltLabel 16 anode_sham_in_after_pdt -gltCode 16 'CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1pdt’
-gltLabel 17 anode_sham_in_after_buyizhi_yizhi -gltCode 17 'CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1buyizhi -1yizhi’
-gltLabel 18 anode_sham_in_after_pmt_pdt -gltCode 18 ‘CiJi : 1anode -1sham QainHou : 1after Contrast3 : 1pmt -1pdt’
-gltLabel 19 CiJi_x_QianHou_buyizhi_or_yizhi -gltCode 19 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1buyizhi +1yizhi’
-gltLabel 20 CiJi_x_QianHou_buyizhi_only -gltCode 20 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1buyizhi’
-gltLabel 21 CiJi_x_QianHou_yizhi_only -gltCode 21 ‘CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1yizhi’
-gltLabel 22 CiJi_x_QianHou_buyizhi_yizhi_3inter -gltCode 22 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1buyizhi -1yizhi’
-gltLabel 23 CiJi_x_QianHou_pmt_or_pdt -gltCode 23 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1pmt +1pdt’
-gltLabel 24 CiJi_x_QianHou_pmt_only -gltCode 24 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1pmt’
-gltLabel 25 CiJi_x_QianHou_pdt_only -gltCode 25 ‘CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1pdt’
-gltLabel 26 CiJi_x_QianHou_pmt_pdt_3inter -gltCode 26 'CiJi : 1anode -1sham QainHou : 1after -1before Contrast3 : 1pmt -1pdt’
-gltLabel 27 anode_sham_in_before_now -gltCode 27 'CiJi : 1anode -1sham QainHou : 1before Contrast3 : 1now’
-gltLabel 28 anode_sham_in_before_notnow -gltCode 28 'CiJi : 1anode -1sham QainHou : 1before Contrast3 : 1notnow’
-gltLabel 29 anode_sham_in_before_buyizhi -gltCode 29 'CiJi : 1anode -1sham QainHou : 1before Contrast3 : 1buyizhi’
-gltLabel 30 anode_sham_in_before_yizhi -gltCode 30 'CiJi : 1anode -1sham QainHou : 1before Contrast3 : 1yizhi’
-gltLabel 31 anode_sham_in_before_pmt -gltCode 31 'CiJi : 1anode -1sham QainHou : 1before Contrast3 : 1pmt’
-gltLabel 32 anode_sham_in_before_pdt -gltCode 32 'CiJi : 1anode -1sham QainHou : 1before Contrast3 : 1pdt’
-gltLabel 33 anode_sham_in_before_buyizhi_yizhi -gltCode 33 'CiJi : 1anode -1sham QainHou : 1before Contrast3 : 1buyizhi -1yizhi’
-gltLabel 34 anode_sham_in_before_pmt_pdt -gltCode 34 ‘CiJi : 1anode -1sham QainHou : 1before Contrast3 : 1pmt -1*pdt’
-dataTable @table2.txt "

This is full information about error:
Read 10809 items
Loading required package: nlme
Package nlme loaded successfully!

Loading required package: phia
Loading required package: car
Loading required package: carData
Package phia loaded successfully!

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***** Summary information of data structure *****
50 subjects : sub02 sub03 sub04 sub05 sub06 sub07 sub09 sub10 sub11 sub12 sub13 sub14 sub15 sub16 sub17 sub18 sub19 sub20 sub21 sub22 sub23 sub24 sub25 sub26 sub27 sub28 sub29 sub30 sub31 sub32 sub33 sub34 sub35 sub36 sub37 sub38 sub39 sub40 sub41 sub42 sub43 sub44 sub45 sub46 sub47 sub48 sub49 sub50 sub51 sub52
1200 response values
2 levels for factor CiJi : anode sham
2 levels for factor QainHou : after before
6 levels for factor Contrast3 : buyizhi notnow now pdt pmt yizhi
2 levels for factor sex : 1 2
1200 centered values for numeric variable age : 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 5.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 3.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 8.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 2.74 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 0.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 -3.26 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 1.74 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -1.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -4.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -2.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26 -0.26
1200 centered values for numeric variable education : 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 8.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 3.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 2.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -4.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 0.54 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 1.54 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -1.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -3.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -2.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46 -0.46
34 post hoc tests

Contingency tables of subject distributions among the categorical variables:

Tabulation of subjects against all categorical variables

Subj vs CiJi:
       
        anode sham
  sub02    12   12
  sub03    12   12
  sub04    12   12
  sub05    12   12
  sub06    12   12
  sub07    12   12
  sub09    12   12
  sub10    12   12
  sub11    12   12
  sub12    12   12
  sub13    12   12
  sub14    12   12
  sub15    12   12
  sub16    12   12
  sub17    12   12
  sub18    12   12
  sub19    12   12
  sub20    12   12
  sub21    12   12
  sub22    12   12
  sub23    12   12
  sub24    12   12
  sub25    12   12
  sub26    12   12
  sub27    12   12
  sub28    12   12
  sub29    12   12
  sub30    12   12
  sub31    12   12
  sub32    12   12
  sub33    12   12
  sub34    12   12
  sub35    12   12
  sub36    12   12
  sub37    12   12
  sub38    12   12
  sub39    12   12
  sub40    12   12
  sub41    12   12
  sub42    12   12
  sub43    12   12
  sub44    12   12
  sub45    12   12
  sub46    12   12
  sub47    12   12
  sub48    12   12
  sub49    12   12
  sub50    12   12
  sub51    12   12
  sub52    12   12

Subj vs QainHou:

    after before

sub02 12 12
sub03 12 12
sub04 12 12
sub05 12 12
sub06 12 12
sub07 12 12
sub09 12 12
sub10 12 12
sub11 12 12
sub12 12 12
sub13 12 12
sub14 12 12
sub15 12 12
sub16 12 12
sub17 12 12
sub18 12 12
sub19 12 12
sub20 12 12
sub21 12 12
sub22 12 12
sub23 12 12
sub24 12 12
sub25 12 12
sub26 12 12
sub27 12 12
sub28 12 12
sub29 12 12
sub30 12 12
sub31 12 12
sub32 12 12
sub33 12 12
sub34 12 12
sub35 12 12
sub36 12 12
sub37 12 12
sub38 12 12
sub39 12 12
sub40 12 12
sub41 12 12
sub42 12 12
sub43 12 12
sub44 12 12
sub45 12 12
sub46 12 12
sub47 12 12
sub48 12 12
sub49 12 12
sub50 12 12
sub51 12 12
sub52 12 12

Subj vs Contrast3:
       
        buyizhi notnow now pdt pmt yizhi
  sub02       4      4   4   4   4     4
  sub03       4      4   4   4   4     4
  sub04       4      4   4   4   4     4
  sub05       4      4   4   4   4     4
  sub06       4      4   4   4   4     4
  sub07       4      4   4   4   4     4
  sub09       4      4   4   4   4     4
  sub10       4      4   4   4   4     4
  sub11       4      4   4   4   4     4
  sub12       4      4   4   4   4     4
  sub13       4      4   4   4   4     4
  sub14       4      4   4   4   4     4
  sub15       4      4   4   4   4     4
  sub16       4      4   4   4   4     4
  sub17       4      4   4   4   4     4
  sub18       4      4   4   4   4     4
  sub19       4      4   4   4   4     4
  sub20       4      4   4   4   4     4
  sub21       4      4   4   4   4     4
  sub22       4      4   4   4   4     4
  sub23       4      4   4   4   4     4
  sub24       4      4   4   4   4     4
  sub25       4      4   4   4   4     4
  sub26       4      4   4   4   4     4
  sub27       4      4   4   4   4     4
  sub28       4      4   4   4   4     4
  sub29       4      4   4   4   4     4
  sub30       4      4   4   4   4     4
  sub31       4      4   4   4   4     4
  sub32       4      4   4   4   4     4
  sub33       4      4   4   4   4     4
  sub34       4      4   4   4   4     4
  sub35       4      4   4   4   4     4
  sub36       4      4   4   4   4     4
  sub37       4      4   4   4   4     4
  sub38       4      4   4   4   4     4
  sub39       4      4   4   4   4     4
  sub40       4      4   4   4   4     4
  sub41       4      4   4   4   4     4
  sub42       4      4   4   4   4     4
  sub43       4      4   4   4   4     4
  sub44       4      4   4   4   4     4
  sub45       4      4   4   4   4     4
  sub46       4      4   4   4   4     4
  sub47       4      4   4   4   4     4
  sub48       4      4   4   4   4     4
  sub49       4      4   4   4   4     4
  sub50       4      4   4   4   4     4
  sub51       4      4   4   4   4     4
  sub52       4      4   4   4   4     4

Subj vs sex:

     1  2

sub02 24 0
sub03 24 0
sub04 24 0
sub05 0 24
sub06 0 24
sub07 0 24
sub09 24 0
sub10 24 0
sub11 24 0
sub12 24 0
sub13 0 24
sub14 0 24
sub15 0 24
sub16 0 24
sub17 0 24
sub18 0 24
sub19 0 24
sub20 0 24
sub21 0 24
sub22 24 0
sub23 0 24
sub24 0 24
sub25 0 24
sub26 24 0
sub27 0 24
sub28 0 24
sub29 0 24
sub30 0 24
sub31 24 0
sub32 24 0
sub33 0 24
sub34 24 0
sub35 24 0
sub36 24 0
sub37 24 0
sub38 24 0
sub39 0 24
sub40 24 0
sub41 24 0
sub42 0 24
sub43 0 24
sub44 0 24
sub45 24 0
sub46 0 24
sub47 24 0
sub48 0 24
sub49 24 0
sub50 24 0
sub51 24 0
sub52 24 0
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now…

Reading input files: Done!

Range of input data: [0.000, 1.810]

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 if (ii < dimx) ii ← ii + 1 else if (jj < dimy) { :
missing value where TRUE/FALSE needed
Execution halted

8

-model “CiJiQainHouContrast3+CiJi:QainHou:age:education”\

The model specification is a little strange for this part:

CiJi:QainHou:age:education

You want this four-way interaction but without the following: main effects of age and education, CiJi:QainHou:age and CiJi:QainHou:education. Could you explain exactly what effects are you looking for?

9

Hi Gang
Thanks for your reply. I tried -model “CiJiQainHouContrast3”, and same error remains:

sub52 24 0
***** End of data structure information *****
++++++++++++++++++++++++++++++++++++++++++++++++++++

Reading input files now…

Reading input files: Done!

Range of input data: [0.000, 1.810]

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 if (ii < dimx) ii ← ii + 1 else if (jj < dimy) { :
missing value where TRUE/FALSE needed
Execution halted

10

Remove the option "-mask …/newaal_50+tlrc ", and see if it works.