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Dear AFNI users-
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:
https://discuss.afni.nimh.nih.gov
Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.
The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.
Sincerely, AFNI HQ
| October 08, 2020 01:19AM | |
Registered: 3 years ago Posts: 5 |
Dear pt
I indeed ran the command
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.19
It returns
ln: failed to create symbolic link '/usr/lib/x86_64-linux-gnu/libgsl.so.19': File exists
System check still returns errors on 3dSkullStrip and 3dRSFC. (please see below)
BTW, I had to execute
sudo apt-get install libglu1
because I got an error
libGLU.so.1: cannot open shared object file: No such file or directory
Back to the R related error:
I down graded to R 3.6 but I still got many errors/warnings after executing rPkgsInstall -pkgs ALL
(please see below under ***** R related issues ******* )
Please let me know if you know how to fix my problems.
thanks
Christine
cslaw@mackeylab1027:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.4.0-48-generic
version: #52-Ubuntu SMP Thu Sep 10 10:58:49 UTC 2020
distribution: Ubuntu 20.04 focal
number of CPUs: 18
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/cslaw/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Oct 2 2020
: AFNI_20.3.00 'Vespasian'
AFNI_version.txt : AFNI_20.3.00, linux_ubuntu_16_64, Oct 02 2020
which python : /usr/bin/python
python version : 2.7.18rc1
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/cslaw/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.8)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
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/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /home/cslaw/sct_4.3/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/cslaw/abin:/home/cslaw/Documents/MATLAB/fmriutil
PYTHONPATH =
R_LIBS = /home/cslaw/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/cslaw/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.2ubuntu0.1 (amd64)
have Ubuntu system: Ubuntu 20.04 focal
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Oct 2 2020
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
****************************** R related issues ****************************************
cslaw@mackeylab1027:~$ rPkgsInstall -pkgs ALL
Installing packages into ‘/home/cslaw/R’
(as ‘lib’ is unspecified)
Warning: dependencies ‘cmdstanr’, ‘foreign’ are not available
also installing the dependencies ‘conquer’, ‘data.table’, ‘httr’, ‘hexbin’, ‘robustbase’, ‘openssl’, ‘igraph’, ‘units’, ‘cluster’, ‘RcppEigen’, ‘quantreg’, ‘rio’, ‘survival’, ‘libcoin’, ‘jpeg’, ‘psych’, ‘rstatix’, ‘TMB’, ‘StanHeaders’, ‘plotly’, ‘qqplotr’, ‘V8’, ‘rsconnect’, ‘threejs’, ‘msm’, ‘gsl’, ‘sf’, ‘expm’, ‘tmvnsim’, ‘RcppArmadillo’, ‘Hmisc’, ‘lme4’, ‘pbkrtest’, ‘car’, ‘coin’, ‘latticeExtra’, ‘mlmRev’, ‘Matrix’, ‘psychTools’, ‘MEMSS’, ‘effects’, ‘ggpubr’, ‘glmmTMB’, ‘rstanarm’, ‘ggResidpanel’, ‘rstan’, ‘mgcv’, ‘shinystan’, ‘nleqslv’, ‘rtdists’, ‘spdep’, ‘mnormt’, ‘MCMCglmm’, ‘splines2’, ‘ape’, ‘arm’
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ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-data.table’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-hexbin’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-robustbase’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-openssl’
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.6-7
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/RtmpRcXr0P/R.INSTALL25d92457a417/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/cslaw/R/units’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-cluster’
* installing *source* package ‘libcoin’ ...
** package ‘libcoin’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/mvtnorm/include" -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libcoin-init.c -o libcoin-init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/mvtnorm/include" -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libcoin.c -o libcoin.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o libcoin.so libcoin-init.o libcoin.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: libcoin.so] Error 1
ERROR: compilation failed for package ‘libcoin’
* removing ‘/home/cslaw/R/libcoin’
* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o
In file included from read.c:1:
rjcommon.h:11:10: fatal error: jpeglib.h: No such file or directory
11 | #include <jpeglib.h>
| ^~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: read.o] Error 1
ERROR: compilation failed for package ‘jpeg’
* removing ‘/home/cslaw/R/jpeg’
* installing *source* package ‘V8’ ...
** package ‘V8’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=-I/usr/include/v8 -I/usr/include/v8-3.14
Using PKG_LIBS=-lv8 -lv8_libplatform
-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find the libv8 engine library. Try installing:
* deb: libv8-dev or libnode-dev (Debian / Ubuntu)
* rpm: v8-devel (Fedora, EPEL)
* brew: v8 (OSX)
* csw: libv8_dev (Solaris)
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
---------------------------[ ERROR MESSAGE ]----------------------------
<stdin>:1:10: fatal error: v8.h: No such file or directory
compilation terminated.
------------------------------------------------------------------------
ERROR: configuration failed for package ‘V8’
* removing ‘/home/cslaw/R/V8’
* 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/cslaw/R/gsl’
* installing *source* package ‘tmvnsim’ ...
** package ‘tmvnsim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Fortran2CWrapper.c -o Fortran2CWrapper.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c tmvnghk.f90 -o tmvnghk.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tmvnsim.so Fortran2CWrapper.o tmvnghk.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: tmvnsim.so] Error 1
ERROR: compilation failed for package ‘tmvnsim’
* removing ‘/home/cslaw/R/tmvnsim’
* 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++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 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... system LAPACK found
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/home/cslaw/R/RcppArmadillo’
* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CHMfactor.c -o CHMfactor.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Csparse.c -o Csparse.o
....
make[2]: Leaving directory '/tmp/RtmpjkT8PB/R.INSTALL2ca8d17e50b/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpjkT8PB/R.INSTALL2ca8d17e50b/Matrix/src/AMD'
make[1]: Entering directory '/tmp/RtmpjkT8PB/R.INSTALL2ca8d17e50b/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[1]: Leaving directory '/tmp/RtmpjkT8PB/R.INSTALL2ca8d17e50b/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/home/cslaw/R/Matrix’
* installing *source* package ‘nleqslv’ ...
** package ‘nleqslv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c lautil.f -o lautil.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c limhpar.f -o limhpar.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c liqrev.f -o liqrev.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c liqrup.f -o liqrup.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c lirslv.f -o lirslv.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nleqslv.c -o nleqslv.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwbjac.f -o nwbjac.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwbrdn.f -o nwbrdn.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwclsh.f -o nwclsh.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwddlg.f -o nwddlg.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwglsh.f -o nwglsh.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwmhlm.f -o nwmhlm.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwnjac.f -o nwnjac.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwnleq.f -o nwnleq.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwnwtn.f -o nwnwtn.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nwout.c -o nwout.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwpdlg.f -o nwpdlg.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwpure.f -o nwpure.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwqlsh.f -o nwqlsh.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwtrup.f -o nwtrup.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwutil.f -o nwutil.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nleqslv.so init.o lautil.o limhpar.o liqrev.o liqrup.o lirslv.o nleqslv.o nwbjac.o nwbrdn.o nwclsh.o nwddlg.o nwglsh.o nwmhlm.o nwnjac.o nwnleq.o nwnwtn.o nwout.o nwpdlg.o nwpure.o nwqlsh.o nwtrup.o nwutil.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: nleqslv.so] Error 1
ERROR: compilation failed for package ‘nleqslv’
* removing ‘/home/cslaw/R/nleqslv’
* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c BIONJ.c -o BIONJ.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c NNI.c -o NNI.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SPR.c -o SPR.o
...
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: ape.so] Error 1
ERROR: compilation failed for package ‘ape’
* removing ‘/home/cslaw/R/ape’
ERROR: dependencies ‘Matrix’, ‘RcppArmadillo’ are not available for package ‘conquer’
* removing ‘/home/cslaw/R/conquer’
ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/home/cslaw/R/httr’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-igraph’
ERROR: dependency ‘Matrix’ is not available for package ‘RcppEigen’
* removing ‘/home/cslaw/R/RcppEigen’
ERROR: dependencies ‘foreign’, ‘data.table’ are not available for package ‘rio’
* removing ‘/home/cslaw/R/rio’
ERROR: dependency ‘Matrix’ is not available for package ‘survival’
* removing ‘/home/cslaw/R/survival’
ERROR: dependency ‘robustbase’ is not available for package ‘qqplotr’
* removing ‘/home/cslaw/R/qqplotr’
ERROR: dependency ‘openssl’ is not available for package ‘rsconnect’
* removing ‘/home/cslaw/R/rsconnect’
ERROR: dependency ‘units’ is not available for package ‘sf’
* removing ‘/home/cslaw/R/sf’
ERROR: dependency ‘Matrix’ is not available for package ‘expm’
* removing ‘/home/cslaw/R/expm’
ERROR: dependency ‘jpeg’ is not available for package ‘latticeExtra’
* removing ‘/home/cslaw/R/latticeExtra’
ERROR: dependency ‘Matrix’ is not available for package ‘mgcv’
* removing ‘/home/cslaw/R/mgcv’
ERROR: dependency ‘tmvnsim’ is not available for package ‘mnormt’
* removing ‘/home/cslaw/R/mnormt’
ERROR: dependencies ‘Matrix’, ‘ape’ are not available for package ‘MCMCglmm’
* removing ‘/home/cslaw/R/MCMCglmm’
ERROR: dependency ‘RcppArmadillo’ is not available for package ‘splines2’
* removing ‘/home/cslaw/R/splines2’
ERROR: dependencies ‘Matrix’, ‘conquer’ are not available for package ‘quantreg’
* removing ‘/home/cslaw/R/quantreg’
ERROR: dependency ‘mnormt’ is not available for package ‘psych’
* removing ‘/home/cslaw/R/psych’
ERROR: dependencies ‘Matrix’, ‘RcppEigen’ are not available for package ‘TMB’
* removing ‘/home/cslaw/R/TMB’
ERROR: dependency ‘RcppEigen’ is not available for package ‘StanHeaders’
* removing ‘/home/cslaw/R/StanHeaders’
ERROR: dependencies ‘httr’, ‘hexbin’, ‘data.table’ are not available for package ‘plotly’
* removing ‘/home/cslaw/R/plotly’
ERROR: dependency ‘igraph’ is not available for package ‘threejs’
* removing ‘/home/cslaw/R/threejs’
ERROR: dependencies ‘survival’, ‘expm’ are not available for package ‘msm’
* removing ‘/home/cslaw/R/msm’
ERROR: dependencies ‘survival’, ‘latticeExtra’, ‘cluster’, ‘foreign’, ‘data.table’ are not available for package ‘Hmisc’
* removing ‘/home/cslaw/R/Hmisc’
ERROR: dependencies ‘Matrix’, ‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/home/cslaw/R/lme4’
ERROR: dependencies ‘survival’, ‘libcoin’ are not available for package ‘coin’
* removing ‘/home/cslaw/R/coin’
ERROR: dependencies ‘sf’, ‘Matrix’, ‘expm’ are not available for package ‘spdep’
* removing ‘/home/cslaw/R/spdep’
ERROR: dependencies ‘lme4’, ‘Matrix’ are not available for package ‘pbkrtest’
* removing ‘/home/cslaw/R/pbkrtest’
ERROR: dependency ‘lme4’ is not available for package ‘mlmRev’
* removing ‘/home/cslaw/R/mlmRev’
ERROR: dependencies ‘foreign’, ‘psych’ are not available for package ‘psychTools’
* removing ‘/home/cslaw/R/psychTools’
ERROR: dependency ‘lme4’ is not available for package ‘MEMSS’
* removing ‘/home/cslaw/R/MEMSS’
ERROR: dependency ‘lme4’ is not available for package ‘effects’
* removing ‘/home/cslaw/R/effects’
ERROR: dependencies ‘TMB’, ‘lme4’, ‘Matrix’, ‘RcppEigen’ are not available for package ‘glmmTMB’
* removing ‘/home/cslaw/R/glmmTMB’
ERROR: dependencies ‘plotly’, ‘qqplotr’ are not available for package ‘ggResidpanel’
* removing ‘/home/cslaw/R/ggResidpanel’
ERROR: dependencies ‘StanHeaders’, ‘V8’, ‘RcppEigen’ are not available for package ‘rstan’
* removing ‘/home/cslaw/R/rstan’
ERROR: dependencies ‘msm’, ‘gsl’ are not available for package ‘rtdists’
* removing ‘/home/cslaw/R/rtdists’
ERROR: dependencies ‘Matrix’, ‘lme4’, ‘Hmisc’ are not available for package ‘arm’
* removing ‘/home/cslaw/R/arm’
ERROR: dependency ‘lme4’ is not available for package ‘lmerTest’
* removing ‘/home/cslaw/R/lmerTest’
ERROR: dependencies ‘mgcv’, ‘pbkrtest’, ‘quantreg’, ‘rio’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/cslaw/R/car’
ERROR: dependencies ‘rsconnect’, ‘rstan’, ‘threejs’ are not available for package ‘shinystan’
* removing ‘/home/cslaw/R/shinystan’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/cslaw/R/rstatix’
ERROR: dependencies ‘lme4’, ‘Matrix’, ‘rstan’, ‘shinystan’, ‘survival’, ‘StanHeaders’, ‘RcppEigen’ are not available for package ‘rstanarm’
* removing ‘/home/cslaw/R/rstanarm’
ERROR: dependencies ‘lme4’, ‘pbkrtest’, ‘lmerTest’, ‘car’ are not available for package ‘afex’
* removing ‘/home/cslaw/R/afex’
ERROR: dependencies ‘car’, ‘Matrix’ are not available for package ‘phia’
* removing ‘/home/cslaw/R/phia’
ERROR: dependencies ‘rstan’, ‘Matrix’, ‘mgcv’, ‘shinystan’, ‘nleqslv’ are not available for package ‘brms’
* removing ‘/home/cslaw/R/brms’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/cslaw/R/ggpubr’
The downloaded source packages are in
‘/tmp/RtmpkOueVY/downloaded_packages’
++ Note: @ 22:06:05
This package has been installed on the computer: afex
This package has been installed on the computer: phia
This package has been installed on the computer: lmerTest
This package has been installed on the computer: brms
There were 50 or more warnings (use warnings() to see the first 50)
I indeed ran the command
sudo ln -s /usr/lib/x86_64-linux-gnu/libgsl.so.23 /usr/lib/x86_64-linux-gnu/libgsl.so.19
It returns
ln: failed to create symbolic link '/usr/lib/x86_64-linux-gnu/libgsl.so.19': File exists
System check still returns errors on 3dSkullStrip and 3dRSFC. (please see below)
BTW, I had to execute
sudo apt-get install libglu1
because I got an error
libGLU.so.1: cannot open shared object file: No such file or directory
Back to the R related error:
I down graded to R 3.6 but I still got many errors/warnings after executing rPkgsInstall -pkgs ALL
(please see below under ***** R related issues ******* )
Please let me know if you know how to fix my problems.
thanks
Christine
cslaw@mackeylab1027:~$ afni_system_check.py -check_all
-------------------------------- general ---------------------------------
architecture: 64bit
system: Linux
release: 5.4.0-48-generic
version: #52-Ubuntu SMP Thu Sep 10 10:58:49 UTC 2020
distribution: Ubuntu 20.04 focal
number of CPUs: 18
apparent login shell: bash
shell RC file: .bashrc (exists)
--------------------- AFNI and related program tests ---------------------
which afni : /home/cslaw/abin/afni
afni version : Precompiled binary linux_ubuntu_16_64: Oct 2 2020
: AFNI_20.3.00 'Vespasian'
AFNI_version.txt : AFNI_20.3.00, linux_ubuntu_16_64, Oct 02 2020
which python : /usr/bin/python
python version : 2.7.18rc1
which R : /usr/bin/R
R version : R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
which tcsh : /usr/bin/tcsh
instances of various programs found in PATH:
afni : 1 (/home/cslaw/abin/afni)
R : 1 (/usr/bin/R)
python : 1 (/usr/bin/python2.7)
python2 : 1 (/usr/bin/python2.7)
python3 : 1 (/usr/bin/python3.8)
testing ability to start various programs...
afni : success
suma : success
3dSkullStrip : FAILURE
3dSkullStrip: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
uber_subject.py : success
3dAllineate : success
3dRSFC : FAILURE
3dRSFC: error while loading shared libraries: libgsl.so.19: cannot open shared object file: No such file or directory
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/lib/R
checking for $HOME files...
.afnirc : found
.sumarc : found
.afni/help/all_progs.COMP : found
------------------------------ python libs -------------------------------
** failed to load module PyQt4
-- PyQt4 is no longer needed for an AFNI bootcamp
** failed to load module matplotlib.pyplot
-- matplotlib.pyplot is not required, but is desirable
-------------------------------- env vars --------------------------------
PATH = /home/cslaw/sct_4.3/bin:/usr/local/fsl/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/cslaw/abin:/home/cslaw/Documents/MATLAB/fmriutil
PYTHONPATH =
R_LIBS = /home/cslaw/R
LD_LIBRARY_PATH =
DYLD_LIBRARY_PATH =
DYLD_FALLBACK_LIBRARY_PATH =
------------------------------ data checks -------------------------------
data dir : missing AFNI_data6
data dir : missing AFNI_demos
data dir : missing suma_demo
data dir : missing afni_handouts
atlas : found TT_N27+tlrc under /home/cslaw/abin
------------------------------ OS specific -------------------------------
which apt-get : /usr/bin/apt-get
apt-get version : apt 2.0.2ubuntu0.1 (amd64)
have Ubuntu system: Ubuntu 20.04 focal
have Ubuntu afni : Precompiled binary linux_ubuntu_16_64: Oct 2 2020
========================= summary, please fix: =========================
* just be aware: login shell 'bash', but our code examples use 'tcsh'
* AFNI programs show FAILURE
* missing R packages (see rPkgsInstall)
* insufficient data for AFNI bootcamp
****************************** R related issues ****************************************
cslaw@mackeylab1027:~$ rPkgsInstall -pkgs ALL
Installing packages into ‘/home/cslaw/R’
(as ‘lib’ is unspecified)
Warning: dependencies ‘cmdstanr’, ‘foreign’ are not available
also installing the dependencies ‘conquer’, ‘data.table’, ‘httr’, ‘hexbin’, ‘robustbase’, ‘openssl’, ‘igraph’, ‘units’, ‘cluster’, ‘RcppEigen’, ‘quantreg’, ‘rio’, ‘survival’, ‘libcoin’, ‘jpeg’, ‘psych’, ‘rstatix’, ‘TMB’, ‘StanHeaders’, ‘plotly’, ‘qqplotr’, ‘V8’, ‘rsconnect’, ‘threejs’, ‘msm’, ‘gsl’, ‘sf’, ‘expm’, ‘tmvnsim’, ‘RcppArmadillo’, ‘Hmisc’, ‘lme4’, ‘pbkrtest’, ‘car’, ‘coin’, ‘latticeExtra’, ‘mlmRev’, ‘Matrix’, ‘psychTools’, ‘MEMSS’, ‘effects’, ‘ggpubr’, ‘glmmTMB’, ‘rstanarm’, ‘ggResidpanel’, ‘rstan’, ‘mgcv’, ‘shinystan’, ‘nleqslv’, ‘rtdists’, ‘spdep’, ‘mnormt’, ‘MCMCglmm’, ‘splines2’, ‘ape’, ‘arm’
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ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-data.table’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-hexbin’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-robustbase’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-openssl’
* installing *source* package ‘units’ ...
** package ‘units’ successfully unpacked and MD5 sums checked
** using staged installation
configure: units: 0.6-7
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/RtmpRcXr0P/R.INSTALL25d92457a417/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/cslaw/R/units’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-cluster’
* installing *source* package ‘libcoin’ ...
** package ‘libcoin’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/mvtnorm/include" -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libcoin-init.c -o libcoin-init.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/mvtnorm/include" -fvisibility=hidden -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libcoin.c -o libcoin.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o libcoin.so libcoin-init.o libcoin.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: libcoin.so] Error 1
ERROR: compilation failed for package ‘libcoin’
* removing ‘/home/cslaw/R/libcoin’
* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c read.c -o read.o
In file included from read.c:1:
rjcommon.h:11:10: fatal error: jpeglib.h: No such file or directory
11 | #include <jpeglib.h>
| ^~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib/R/etc/Makeconf:168: read.o] Error 1
ERROR: compilation failed for package ‘jpeg’
* removing ‘/home/cslaw/R/jpeg’
* installing *source* package ‘V8’ ...
** package ‘V8’ successfully unpacked and MD5 sums checked
** using staged installation
Using PKG_CFLAGS=-I/usr/include/v8 -I/usr/include/v8-3.14
Using PKG_LIBS=-lv8 -lv8_libplatform
-----------------------------[ ANTICONF ]-------------------------------
Configuration failed to find the libv8 engine library. Try installing:
* deb: libv8-dev or libnode-dev (Debian / Ubuntu)
* rpm: v8-devel (Fedora, EPEL)
* brew: v8 (OSX)
* csw: libv8_dev (Solaris)
To use a custom libv8, set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
---------------------------[ ERROR MESSAGE ]----------------------------
<stdin>:1:10: fatal error: v8.h: No such file or directory
compilation terminated.
------------------------------------------------------------------------
ERROR: configuration failed for package ‘V8’
* removing ‘/home/cslaw/R/V8’
* 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/cslaw/R/gsl’
* installing *source* package ‘tmvnsim’ ...
** package ‘tmvnsim’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Fortran2CWrapper.c -o Fortran2CWrapper.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c tmvnghk.f90 -o tmvnghk.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o tmvnsim.so Fortran2CWrapper.o tmvnghk.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: tmvnsim.so] Error 1
ERROR: compilation failed for package ‘tmvnsim’
* removing ‘/home/cslaw/R/tmvnsim’
* 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++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 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... system LAPACK found
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -I../inst/include -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: RcppArmadillo.so] Error 1
ERROR: compilation failed for package ‘RcppArmadillo’
* removing ‘/home/cslaw/R/RcppArmadillo’
* installing *source* package ‘Matrix’ ...
** package ‘Matrix’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CHMfactor.c -o CHMfactor.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -I./SuiteSparse_config -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Csparse.c -o Csparse.o
....
make[2]: Leaving directory '/tmp/RtmpjkT8PB/R.INSTALL2ca8d17e50b/Matrix/src/AMD/Source'
make[1]: Leaving directory '/tmp/RtmpjkT8PB/R.INSTALL2ca8d17e50b/Matrix/src/AMD'
make[1]: Entering directory '/tmp/RtmpjkT8PB/R.INSTALL2ca8d17e50b/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -DNTIMER -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SuiteSparse_config.c -o SuiteSparse_config.o
ar -rucs ../SuiteSparse_config.a SuiteSparse_config.o
ar: `u' modifier ignored since `D' is the default (see `U')
make[1]: Leaving directory '/tmp/RtmpjkT8PB/R.INSTALL2ca8d17e50b/Matrix/src/SuiteSparse_config'
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Matrix.so CHMfactor.o Csparse.o TMatrix_as.o Tsparse.o init.o Mutils.o chm_common.o cs.o cs_utils.o dense.o dgCMatrix.o dgTMatrix.o dgeMatrix.o dpoMatrix.o dppMatrix.o dsCMatrix.o dsyMatrix.o dspMatrix.o dtCMatrix.o dtTMatrix.o dtrMatrix.o dtpMatrix.o factorizations.o ldense.o lgCMatrix.o sparseQR.o abIndex.o CHOLMOD.a COLAMD.a AMD.a SuiteSparse_config.a -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: Matrix.so] Error 1
ERROR: compilation failed for package ‘Matrix’
* removing ‘/home/cslaw/R/Matrix’
* installing *source* package ‘nleqslv’ ...
** package ‘nleqslv’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c lautil.f -o lautil.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c limhpar.f -o limhpar.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c liqrev.f -o liqrev.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c liqrup.f -o liqrup.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c lirslv.f -o lirslv.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nleqslv.c -o nleqslv.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwbjac.f -o nwbjac.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwbrdn.f -o nwbrdn.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwclsh.f -o nwclsh.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwddlg.f -o nwddlg.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwglsh.f -o nwglsh.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwmhlm.f -o nwmhlm.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwnjac.f -o nwnjac.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwnleq.f -o nwnleq.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwnwtn.f -o nwnwtn.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nwout.c -o nwout.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwpdlg.f -o nwpdlg.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwpure.f -o nwpure.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwqlsh.f -o nwqlsh.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwtrup.f -o nwtrup.o
gfortran -fno-optimize-sibling-calls -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -c nwutil.f -o nwutil.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o nleqslv.so init.o lautil.o limhpar.o liqrev.o liqrup.o lirslv.o nleqslv.o nwbjac.o nwbrdn.o nwclsh.o nwddlg.o nwglsh.o nwmhlm.o nwnjac.o nwnleq.o nwnwtn.o nwout.o nwpdlg.o nwpure.o nwqlsh.o nwtrup.o nwutil.o -llapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: nleqslv.so] Error 1
ERROR: compilation failed for package ‘nleqslv’
* removing ‘/home/cslaw/R/nleqslv’
* installing *source* package ‘ape’ ...
** package ‘ape’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c BIONJ.c -o BIONJ.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c NNI.c -o NNI.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -I"/home/cslaw/R/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-jbaK_j/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SPR.c -o SPR.o
...
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o ape.so BIONJ.o NNI.o RcppExports.o SPR.o additive.o ape.o bNNI.o bionjs.o bipartition.o bitsplits.o delta_plot.o dist_dna.o dist_nodes.o ewLasso.o heap.o mat_expo.o me.o me_balanced.o me_ols.o mvr.o mvrs.o nj.o njs.o pic.o plot_phylo.o prop_part.o rTrait.o read_dna.o reorder_Rcpp.o reorder_phylo.o treePop.o tree_build.o tree_phylo.o triangMtd.o triangMtds.o ultrametric.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -llapack
/usr/bin/ld: cannot find -lblas
collect2: error: ld returned 1 exit status
make: *** [/usr/share/R/share/make/shlib.mk:6: ape.so] Error 1
ERROR: compilation failed for package ‘ape’
* removing ‘/home/cslaw/R/ape’
ERROR: dependencies ‘Matrix’, ‘RcppArmadillo’ are not available for package ‘conquer’
* removing ‘/home/cslaw/R/conquer’
ERROR: dependency ‘openssl’ is not available for package ‘httr’
* removing ‘/home/cslaw/R/httr’
ERROR: failed to lock directory ‘/home/cslaw/R’ for modifying
Try removing ‘/home/cslaw/R/00LOCK-igraph’
ERROR: dependency ‘Matrix’ is not available for package ‘RcppEigen’
* removing ‘/home/cslaw/R/RcppEigen’
ERROR: dependencies ‘foreign’, ‘data.table’ are not available for package ‘rio’
* removing ‘/home/cslaw/R/rio’
ERROR: dependency ‘Matrix’ is not available for package ‘survival’
* removing ‘/home/cslaw/R/survival’
ERROR: dependency ‘robustbase’ is not available for package ‘qqplotr’
* removing ‘/home/cslaw/R/qqplotr’
ERROR: dependency ‘openssl’ is not available for package ‘rsconnect’
* removing ‘/home/cslaw/R/rsconnect’
ERROR: dependency ‘units’ is not available for package ‘sf’
* removing ‘/home/cslaw/R/sf’
ERROR: dependency ‘Matrix’ is not available for package ‘expm’
* removing ‘/home/cslaw/R/expm’
ERROR: dependency ‘jpeg’ is not available for package ‘latticeExtra’
* removing ‘/home/cslaw/R/latticeExtra’
ERROR: dependency ‘Matrix’ is not available for package ‘mgcv’
* removing ‘/home/cslaw/R/mgcv’
ERROR: dependency ‘tmvnsim’ is not available for package ‘mnormt’
* removing ‘/home/cslaw/R/mnormt’
ERROR: dependencies ‘Matrix’, ‘ape’ are not available for package ‘MCMCglmm’
* removing ‘/home/cslaw/R/MCMCglmm’
ERROR: dependency ‘RcppArmadillo’ is not available for package ‘splines2’
* removing ‘/home/cslaw/R/splines2’
ERROR: dependencies ‘Matrix’, ‘conquer’ are not available for package ‘quantreg’
* removing ‘/home/cslaw/R/quantreg’
ERROR: dependency ‘mnormt’ is not available for package ‘psych’
* removing ‘/home/cslaw/R/psych’
ERROR: dependencies ‘Matrix’, ‘RcppEigen’ are not available for package ‘TMB’
* removing ‘/home/cslaw/R/TMB’
ERROR: dependency ‘RcppEigen’ is not available for package ‘StanHeaders’
* removing ‘/home/cslaw/R/StanHeaders’
ERROR: dependencies ‘httr’, ‘hexbin’, ‘data.table’ are not available for package ‘plotly’
* removing ‘/home/cslaw/R/plotly’
ERROR: dependency ‘igraph’ is not available for package ‘threejs’
* removing ‘/home/cslaw/R/threejs’
ERROR: dependencies ‘survival’, ‘expm’ are not available for package ‘msm’
* removing ‘/home/cslaw/R/msm’
ERROR: dependencies ‘survival’, ‘latticeExtra’, ‘cluster’, ‘foreign’, ‘data.table’ are not available for package ‘Hmisc’
* removing ‘/home/cslaw/R/Hmisc’
ERROR: dependencies ‘Matrix’, ‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/home/cslaw/R/lme4’
ERROR: dependencies ‘survival’, ‘libcoin’ are not available for package ‘coin’
* removing ‘/home/cslaw/R/coin’
ERROR: dependencies ‘sf’, ‘Matrix’, ‘expm’ are not available for package ‘spdep’
* removing ‘/home/cslaw/R/spdep’
ERROR: dependencies ‘lme4’, ‘Matrix’ are not available for package ‘pbkrtest’
* removing ‘/home/cslaw/R/pbkrtest’
ERROR: dependency ‘lme4’ is not available for package ‘mlmRev’
* removing ‘/home/cslaw/R/mlmRev’
ERROR: dependencies ‘foreign’, ‘psych’ are not available for package ‘psychTools’
* removing ‘/home/cslaw/R/psychTools’
ERROR: dependency ‘lme4’ is not available for package ‘MEMSS’
* removing ‘/home/cslaw/R/MEMSS’
ERROR: dependency ‘lme4’ is not available for package ‘effects’
* removing ‘/home/cslaw/R/effects’
ERROR: dependencies ‘TMB’, ‘lme4’, ‘Matrix’, ‘RcppEigen’ are not available for package ‘glmmTMB’
* removing ‘/home/cslaw/R/glmmTMB’
ERROR: dependencies ‘plotly’, ‘qqplotr’ are not available for package ‘ggResidpanel’
* removing ‘/home/cslaw/R/ggResidpanel’
ERROR: dependencies ‘StanHeaders’, ‘V8’, ‘RcppEigen’ are not available for package ‘rstan’
* removing ‘/home/cslaw/R/rstan’
ERROR: dependencies ‘msm’, ‘gsl’ are not available for package ‘rtdists’
* removing ‘/home/cslaw/R/rtdists’
ERROR: dependencies ‘Matrix’, ‘lme4’, ‘Hmisc’ are not available for package ‘arm’
* removing ‘/home/cslaw/R/arm’
ERROR: dependency ‘lme4’ is not available for package ‘lmerTest’
* removing ‘/home/cslaw/R/lmerTest’
ERROR: dependencies ‘mgcv’, ‘pbkrtest’, ‘quantreg’, ‘rio’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/cslaw/R/car’
ERROR: dependencies ‘rsconnect’, ‘rstan’, ‘threejs’ are not available for package ‘shinystan’
* removing ‘/home/cslaw/R/shinystan’
ERROR: dependency ‘car’ is not available for package ‘rstatix’
* removing ‘/home/cslaw/R/rstatix’
ERROR: dependencies ‘lme4’, ‘Matrix’, ‘rstan’, ‘shinystan’, ‘survival’, ‘StanHeaders’, ‘RcppEigen’ are not available for package ‘rstanarm’
* removing ‘/home/cslaw/R/rstanarm’
ERROR: dependencies ‘lme4’, ‘pbkrtest’, ‘lmerTest’, ‘car’ are not available for package ‘afex’
* removing ‘/home/cslaw/R/afex’
ERROR: dependencies ‘car’, ‘Matrix’ are not available for package ‘phia’
* removing ‘/home/cslaw/R/phia’
ERROR: dependencies ‘rstan’, ‘Matrix’, ‘mgcv’, ‘shinystan’, ‘nleqslv’ are not available for package ‘brms’
* removing ‘/home/cslaw/R/brms’
ERROR: dependency ‘rstatix’ is not available for package ‘ggpubr’
* removing ‘/home/cslaw/R/ggpubr’
The downloaded source packages are in
‘/tmp/RtmpkOueVY/downloaded_packages’
++ Note: @ 22:06:05
This package has been installed on the computer: afex
This package has been installed on the computer: phia
This package has been installed on the computer: lmerTest
This package has been installed on the computer: brms
There were 50 or more warnings (use warnings() to see the first 50)
| Subject | Author | Posted |
|---|---|---|
|
cslaw | October 05, 2020 08:42PM |
|
ptaylor | October 06, 2020 09:32AM |
|
cslaw | October 08, 2020 01:19AM |
|
ptaylor | October 08, 2020 10:40AM |
|
rick reynolds | October 08, 2020 04:22PM |
|
cslaw | October 08, 2020 07:40PM |
|
rick reynolds | October 15, 2020 02:10PM |
|
rick reynolds | October 15, 2020 03:22PM |
