[R-sig-Debian] Installing sjPlot in R 3.4.4 on Ubuntu 16.04LTS

[Brandon C. Zicha]

Dear all,

I have had some rather serious difficulties getting graphics and analysis
packages to load in R on my new Ubuntu Install.

The trouble seems to begin when attempting to install TMB.

I have done a full purge of r-base r-base-dev and r-base-core and
reinstalled the newest version of RStudio (not that this should matter).
I'm not sure what to try next.

many thanks!

Brandon Z

> install.packages("sjPlot")Installing package into ‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)also installing the dependencies ‘TMB’,
‘blme’, ‘arm’, ‘effects’, ‘ggeffects’, ‘glmmTMB’, ‘lme4’, ‘merTools’,
‘sjstats’
trying URL 'https://cloud.r-project.org/src/contrib/TMB_1.7.14.tar.gz'Content
type 'application/x-gzip' length 606414 bytes (592
KB)==================================================downloaded 592 KB
trying URL 'https://cloud.r-project.org/src/contrib/blme_1.0-4.tar.gz'Content
type 'application/x-gzip' length 35054 bytes (34
KB)==================================================downloaded 34 KB
trying URL 'https://cloud.r-project.org/src/contrib/arm_1.10-1.tar.gz'Content
type 'application/x-gzip' length 78301 bytes (76
KB)==================================================downloaded 76 KB
trying URL 'https://cloud.r-project.org/src/contrib/effects_4.0-2.tar.gz'Content
type 'application/x-gzip' length 2021373 bytes (1.9
MB)==================================================downloaded 1.9 MB
trying URL 'https://cloud.r-project.org/src/contrib/ggeffects_0.3.4.tar.gz'Content
type 'application/x-gzip' length 239215 bytes (233
KB)==================================================downloaded 233 KB
trying URL 'https://cloud.r-project.org/src/contrib/glmmTMB_0.2.1.0.tar.gz'Content
type 'application/x-gzip' length 783833 bytes (765
KB)==================================================downloaded 765 KB
trying URL 'https://cloud.r-project.org/src/contrib/lme4_1.1-17.tar.gz'Content
type 'application/x-gzip' length 4103343 bytes (3.9
MB)==================================================downloaded 3.9 MB
trying URL 'https://cloud.r-project.org/src/contrib/merTools_0.4.1.tar.gz'Content
type 'application/x-gzip' length 476671 bytes (465
KB)==================================================downloaded 465 KB
trying URL 'https://cloud.r-project.org/src/contrib/sjstats_0.15.0.tar.gz'Content
type 'application/x-gzip' length 339472 bytes (331
KB)==================================================downloaded 331 KB
trying URL 'https://cloud.r-project.org/src/contrib/sjPlot_2.4.1.tar.gz'Content
type 'application/x-gzip' length 776902 bytes (758
KB)==================================================downloaded 758 KB
* installing *source* package ‘TMB’ ...** package ‘TMB’ successfully
unpacked and MD5 sums checked** libsgcc -std=gnu99
-I/usr/share/R/include -DNDEBUG  -I"/usr/lib/R/library/Matrix/include"
-I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/RcppEigen/include"
-fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c
external_metis.c -o external_metis.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/usr/lib/R/library/Matrix/include"
-I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/RcppEigen/include"
-fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c
-o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/usr/lib/R/library/Matrix/include"
-I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/RcppEigen/include"
-fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c
local_stubs.c -o local_stubs.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/usr/lib/R/library/Matrix/include"
-I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/RcppEigen/include"
-fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c
solve_subset.c -o solve_subset.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG
-I"/usr/lib/R/library/Matrix/include"
-I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/RcppEigen/include"
-fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c
-o utils.o
g++ -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o
TMB.so external_metis.o init.o local_stubs.o solve_subset.o utils.o
-llapack -lblas -lgfortran -lm -lquadmath -fopenmp -L/usr/lib/R/lib
-lRinstalling to
/home/drz/R/x86_64-pc-linux-gnu-library/3.4/TMB/libs** R** inst**
preparing package for lazy loading** help*** installing help indices**
building package indices** testing if installed package can be
loadedBuilding example simple
g++  -I/usr/share/R/include -DNDEBUG
-I/home/drz/R/x86_64-pc-linux-gnu-library/3.4/TMB/include -I
-DTMB_SAFEBOUNDS -DLIB_UNLOAD=R_unload_simple
-DTMB_LIB_INIT=R_init_simple  -I"/usr/lib/R/library/Matrix/include"
-I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/RcppEigen/include"
-fpic  -g -O2 -fstack-protector-strong -Wformat
-Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c
simple.cpp -o simple.o
In file included from simple.cpp:2:0:
/home/drz/R/x86_64-pc-linux-gnu-library/3.4/TMB/include/TMB.hpp:53:23:
fatal error: Eigen/Dense: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:168: recipe for target 'simple.o' failed
make: *** [simple.o] Error 1
Timing stopped at: 0.028 0.004 0.044
Error: package or namespace load failed for ‘TMB’:
 .onAttach failed in attachNamespace() for 'TMB', details:
  call: compile(paste0(name, ".cpp"), ...)
  error: Compilation failed
Error: loading failed
Execution haltedERROR: loading failed* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/TMB’Warning in
install.packages :
  installation of package ‘TMB’ had non-zero exit status* installing
*source* package ‘lme4’ ...** package ‘lme4’ successfully unpacked and
MD5 sums checked** libsg++  -I/usr/share/R/include -DNDEBUG
-I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/Rcpp/include"
-I"/home/drz/R/x86_64-pc-linux-gnu-library/3.4/RcppEigen/include"
-DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -g -O2 -fstack-protector-strong
-Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
-c external.cpp -o external.oIn file included from external.cpp:8:0:
predModule.h:12:23: fatal error: RcppEigen.h: No such file or directory
compilation terminated./usr/lib/R/etc/Makeconf:168: recipe for target
'external.o' failedmake: *** [external.o] Error 1ERROR: compilation
failed for package ‘lme4’* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/lme4’Warning in
install.packages :
  installation of package ‘lme4’ had non-zero exit statusERROR:
dependency ‘lme4’ is not available for package ‘blme’* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/blme’Warning in
install.packages :
  installation of package ‘blme’ had non-zero exit statusERROR:
dependency ‘lme4’ is not available for package ‘arm’* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/arm’Warning in
install.packages :
  installation of package ‘arm’ had non-zero exit statusERROR:
dependency ‘lme4’ is not available for package ‘effects’* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/effects’Warning in
install.packages :
  installation of package ‘effects’ had non-zero exit statusERROR:
dependencies ‘TMB’, ‘lme4’ are not available for package ‘glmmTMB’*
removing ‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/glmmTMB’Warning
in install.packages :
  installation of package ‘glmmTMB’ had non-zero exit statusERROR:
dependencies ‘arm’, ‘lme4’, ‘blme’ are not available for package
‘merTools’* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/merTools’Warning in
install.packages :
  installation of package ‘merTools’ had non-zero exit statusERROR:
dependencies ‘lme4’, ‘glmmTMB’ are not available for package
‘sjstats’* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/sjstats’Warning in
install.packages :
  installation of package ‘sjstats’ had non-zero exit statusERROR:
dependencies ‘effects’, ‘sjstats’ are not available for package
‘ggeffects’* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/ggeffects’Warning in
install.packages :
  installation of package ‘ggeffects’ had non-zero exit statusERROR:
dependencies ‘arm’, ‘effects’, ‘ggeffects’, ‘glmmTMB’, ‘lme4’,
‘merTools’, ‘sjstats’ are not available for package ‘sjPlot’* removing
‘/home/drz/R/x86_64-pc-linux-gnu-library/3.4/sjPlot’Warning in
install.packages :
  installation of package ‘sjPlot’ had non-zero exit statusThe
downloaded source packages are in
	‘/tmp/Rtmpe0EXSm/downloaded_packages’

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