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’ [[alternative HTML version deleted]] _______________________________________________ R-SIG-Debian mailing list R-SIG-Debian@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-debian