rundel@tbBook [gp_pm25]$ docker images REPOSITORY TAG IMAGE ID CREATED SIZE rocker/tidyverse 3.5.2 61266dee5826 8 hours ago 1.86GB rocker/tidyverse latest 61266dee5826 8 hours ago 1.86GB ubuntu 18.10 88fdd57278f5 8 days ago 73.7MB rundel@tbBook [gp_pm25]$ docker run --rm -it rocker/tidyverse /bin/bash root@843af006d51b:/# inst install install2.r installGithub.r installkernel instmodsh root@843af006d51b:/# install2.r spBayes also installing the dependencies ‘coda’, ‘magic’, ‘abind’, ‘Formula’ trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/coda_0.19-2.tar.gz' Content type 'application/octet-stream' length 73530 bytes (71 KB) ================================================== downloaded 71 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/magic_1.5-9.tar.gz' Content type 'application/octet-stream' length 150612 bytes (147 KB) ================================================== downloaded 147 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/abind_1.4-5.tar.gz' Content type 'application/octet-stream' length 21810 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/Formula_1.2-3.tar.gz' Content type 'application/octet-stream' length 151340 bytes (147 KB) ================================================== downloaded 147 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/spBayes_0.4-1.tar.gz' Content type 'application/octet-stream' length 496081 bytes (484 KB) ================================================== downloaded 484 KB * installing *source* package ‘coda’ ... ** package ‘coda’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (coda) * installing *source* package ‘abind’ ... ** package ‘abind’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (abind) * installing *source* package ‘Formula’ ... ** package ‘Formula’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Formula) * installing *source* package ‘magic’ ... ** package ‘magic’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (magic) * installing *source* package ‘spBayes’ ... ** package ‘spBayes’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c adaptMetropGibbs.cpp -o adaptMetropGibbs.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c idist.cpp -o idist.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mkSpCov.cpp -o mkSpCov.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nonSpGLM_AMCMC.cpp -o nonSpGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptsInPoly.cpp -o ptsInPoly.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spDynLM.cpp -o spDynLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spGLM.cpp -o spGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spGLM_AMCMC.cpp -o spGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLM.cpp -o spLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLMPredict.cpp -o spLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLMRecover.cpp -o spLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMPPMvDIC.cpp -o spMPPMvDIC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalign.cpp -o spMisalign.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignGLM.cpp -o spMisalignGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignGLMPredict.cpp -o spMisalignGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignPredict.cpp -o spMisalignPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignRecover.cpp -o spMisalignRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLM.cpp -o spMvGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLMPredict.cpp -o spMvGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLM_AMCMC.cpp -o spMvGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLM.cpp -o spMvLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLMPredict.cpp -o spMvLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLMRecover.cpp -o spMvLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPDynLM.cpp -o spPPDynLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPGLM.cpp -o spPPGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPGLM_AMCMC.cpp -o spPPGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLM.cpp -o spPPLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLMPredict.cpp -o spPPLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLMRecover.cpp -o spPPLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLM.cpp -o spPPMvGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLMPredict.cpp -o spPPMvGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLM_AMCMC.cpp -o spPPMvGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLM.cpp -o spPPMvLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLMPredict.cpp -o spPPMvLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLMRecover.cpp -o spPPMvLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.cpp -o util.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o spBayes.so adaptMetropGibbs.o idist.o init.o mkSpCov.o nonSpGLM_AMCMC.o ptsInPoly.o spDynLM.o spGLM.o spGLM_AMCMC.o spLM.o spLMPredict.o spLMRecover.o spMPPMvDIC.o spMisalign.o spMisalignGLM.o spMisalignGLMPredict.o spMisalignPredict.o spMisalignRecover.o spMvGLM.o spMvGLMPredict.o spMvGLM_AMCMC.o spMvLM.o spMvLMPredict.o spMvLMRecover.o spPPDynLM.o spPPGLM.o spPPGLM_AMCMC.o spPPLM.o spPPLMPredict.o spPPLMRecover.o spPPMvGLM.o spPPMvGLMPredict.o spPPMvGLM_AMCMC.o spPPMvLM.o spPPMvLMPredict.o spPPMvLMRecover.o util.o -L/usr/local/lib/R/lib -lRlapack -lblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/spBayes/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (spBayes) The downloaded source packages are in ‘/tmp/downloaded_packages’ root@843af006d51b:/# root@843af006d51b:/# R R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(spBayes) Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula > root@843af006d51b:/# install2.r --dep TRUE spBayes ^C root@843af006d51b:/# install2.r --deps TRUE spBayes also installing the dependencies ‘RandomFieldsUtils’, ‘sp’, ‘splancs’, ‘RandomFields’, ‘MBA’, ‘geoR’ trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/RandomFieldsUtils_0.3.25.tar.gz' Content type 'application/octet-stream' length 111100 bytes (108 KB) ================================================== downloaded 108 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/sp_1.3-1.tar.gz' Content type 'application/octet-stream' length 1133621 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/splancs_2.01-40.tar.gz' Content type 'application/octet-stream' length 105583 bytes (103 KB) ================================================== downloaded 103 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/RandomFields_3.1.50.tar.gz' Content type 'application/octet-stream' length 1783992 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/MBA_0.0-9.tar.gz' Content type 'application/octet-stream' length 140993 bytes (137 KB) ================================================== downloaded 137 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/geoR_1.7-5.2.1.tar.gz' Content type 'application/octet-stream' length 413766 bytes (404 KB) ================================================== downloaded 404 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/spBayes_0.4-1.tar.gz' Content type 'application/octet-stream' length 496081 bytes (484 KB) ================================================== downloaded 484 KB * installing *source* package ‘RandomFieldsUtils’ ... ** package ‘RandomFieldsUtils’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RFoptions.cc -o RFoptions.o f95 -fpic -g -O2 -c bckslvmodified.f -o bckslvmodified.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c brdomain.cc -o brdomain.o f95 -fpic -g -O2 -c cholmodified.f -o cholmodified.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c diffusion.cc -o diffusion.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init_RandomFieldsUtils.c -o init_RandomFieldsUtils.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kleinkram.cc -o kleinkram.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c maths.cc -o maths.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c options.cc -o options.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c own.cc -o own.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scalar.cc -o scalar.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c solve.cc -o solve.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sort.cc -o sort.o f95 -fpic -g -O2 -c spamown.f -o spamown.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.cc -o utils.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c win_linux_aux.cc -o win_linux_aux.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RandomFieldsUtils.so RFoptions.o bckslvmodified.o brdomain.o cholmodified.o diffusion.o init_RandomFieldsUtils.o kleinkram.o maths.o options.o own.o scalar.o solve.o sort.o spamown.o utils.o win_linux_aux.o -fopenmp -L/usr/local/lib/R/lib -lRlapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RandomFieldsUtils/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (RandomFieldsUtils) * installing *source* package ‘sp’ ... ** package ‘sp’ successfully unpacked and MD5 sums checked ** libs gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcentroid.c -o Rcentroid.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gcdist.c -o gcdist.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pip.c -o pip.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pip2.c -o pip2.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sp_xports.c -o sp_xports.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c surfaceArea.c -o surfaceArea.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zerodist.c -o zerodist.o gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/sp/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (sp) * installing *source* package ‘MBA’ ... ** package ‘MBA’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MBA.cpp -o MBA.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MBAPoints.cpp -o MBAPoints.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MBASurf.cpp -o MBASurf.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MBAdata.cpp -o MBAdata.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c UCBsplineSurface.cpp -o UCBsplineSurface.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c UCBsplines.cpp -o UCBsplines.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o MBA.so MBA.o MBAPoints.o MBASurf.o MBAdata.o UCBsplineSurface.o UCBsplines.o init.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/MBA/libs ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (MBA) * installing *source* package ‘spBayes’ ... ** package ‘spBayes’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c adaptMetropGibbs.cpp -o adaptMetropGibbs.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c idist.cpp -o idist.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mkSpCov.cpp -o mkSpCov.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nonSpGLM_AMCMC.cpp -o nonSpGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptsInPoly.cpp -o ptsInPoly.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spDynLM.cpp -o spDynLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spGLM.cpp -o spGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spGLM_AMCMC.cpp -o spGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLM.cpp -o spLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLMPredict.cpp -o spLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLMRecover.cpp -o spLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMPPMvDIC.cpp -o spMPPMvDIC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalign.cpp -o spMisalign.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignGLM.cpp -o spMisalignGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignGLMPredict.cpp -o spMisalignGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignPredict.cpp -o spMisalignPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignRecover.cpp -o spMisalignRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLM.cpp -o spMvGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLMPredict.cpp -o spMvGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLM_AMCMC.cpp -o spMvGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLM.cpp -o spMvLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLMPredict.cpp -o spMvLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLMRecover.cpp -o spMvLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPDynLM.cpp -o spPPDynLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPGLM.cpp -o spPPGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPGLM_AMCMC.cpp -o spPPGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLM.cpp -o spPPLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLMPredict.cpp -o spPPLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLMRecover.cpp -o spPPLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLM.cpp -o spPPMvGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLMPredict.cpp -o spPPMvGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLM_AMCMC.cpp -o spPPMvGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLM.cpp -o spPPMvLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLMPredict.cpp -o spPPMvLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLMRecover.cpp -o spPPMvLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.cpp -o util.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o spBayes.so adaptMetropGibbs.o idist.o init.o mkSpCov.o nonSpGLM_AMCMC.o ptsInPoly.o spDynLM.o spGLM.o spGLM_AMCMC.o spLM.o spLMPredict.o spLMRecover.o spMPPMvDIC.o spMisalign.o spMisalignGLM.o spMisalignGLMPredict.o spMisalignPredict.o spMisalignRecover.o spMvGLM.o spMvGLMPredict.o spMvGLM_AMCMC.o spMvLM.o spMvLMPredict.o spMvLMRecover.o spPPDynLM.o spPPGLM.o spPPGLM_AMCMC.o spPPLM.o spPPLMPredict.o spPPLMRecover.o spPPMvGLM.o spPPMvGLMPredict.o spPPMvGLM_AMCMC.o spPPMvLM.o spPPMvLMPredict.o spPPMvLMRecover.o util.o -L/usr/local/lib/R/lib -lRlapack -lblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/spBayes/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (spBayes) * installing *source* package ‘splancs’ ... ** package ‘splancs’ successfully unpacked and MD5 sums checked ** libs f95 -fpic -g -O2 -c areapl.f -o areapl.o f95 -fpic -g -O2 -c cncvwt.f -o cncvwt.o f95 -fpic -g -O2 -c dokhat.f -o dokhat.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o f95 -fpic -g -O2 -c inpip.f -o inpip.o f95 -fpic -g -O2 -c ipippa.f -o ipippa.o f95 -fpic -g -O2 -c iplace.f -o iplace.o f95 -fpic -g -O2 -c k12hat.f -o k12hat.o f95 -fpic -g -O2 -c kernel3d.f -o kernel3d.o f95 -fpic -g -O2 -c khvc.f -o khvc.o f95 -fpic -g -O2 -c khvmat.f -o khvmat.o f95 -fpic -g -O2 -c krnnrm.f -o krnnrm.o f95 -fpic -g -O2 -c krnqne.f -o krnqne.o f95 -fpic -g -O2 -c krnqrt.f -o krnqrt.o f95 -fpic -g -O2 -c nndist.f -o nndist.o f95 -fpic -g -O2 -c plarea.f -o plarea.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptinpoly.c -o ptinpoly.o f95 -fpic -g -O2 -c sekhat.f -o sekhat.o f95 -fpic -g -O2 -c sort.f -o sort.o f95 -fpic -g -O2 -c sort2.f -o sort2.o f95 -fpic -g -O2 -c stkhat.f -o stkhat.o f95 -fpic -g -O2 -c stsecal.f -o stsecal.o f95 -fpic -g -O2 -c tribble.f -o tribble.o f95 -fpic -g -O2 -c twodimmse.f -o twodimmse.o f95 -fpic -g -O2 -c weight.f -o weight.o gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o splancs.so areapl.o cncvwt.o dokhat.o init.o inpip.o ipippa.o iplace.o k12hat.o kernel3d.o khvc.o khvmat.o krnnrm.o krnqne.o krnqrt.o nndist.o plarea.o ptinpoly.o sekhat.o sort.o sort2.o stkhat.o stsecal.o tribble.o twodimmse.o weight.o -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/splancs/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (splancs) * installing *source* package ‘RandomFields’ ... ** package ‘RandomFields’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c AutoRandomFields.cc -o AutoRandomFields.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Brown.cc -o Brown.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Coordinate_systems.cc -o Coordinate_systems.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c D.H.cc -o D.H.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Gneiting.cc -o Gneiting.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Huetchen.cc -o Huetchen.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c InternalCov.cc -o InternalCov.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c KeyInfo.cc -o KeyInfo.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MLE.cc -o MLE.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PoissonPolygon.cc -o PoissonPolygon.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Primitive.cc -o Primitive.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c QMath.cc -o QMath.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Specific.cc -o Specific.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SpherModels.cc -o SpherModels.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SpherModelsInitNerror.cc -o SpherModelsInitNerror.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Xempvario.cc -o Xempvario.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c auxiliary.cc -o auxiliary.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c avltr_modified.cc -o avltr_modified.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c circulant.cc -o circulant.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c convhull2D.cc -o convhull2D.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cubicsolver.cc -o cubicsolver.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c direct.cc -o direct.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c empvario.cc -o empvario.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c extremes.cc -o extremes.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c families.cc -o families.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fft.c -o fft.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fftVario.cc -o fftVario.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gauss.cc -o gauss.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gausslikeli.cc -o gausslikeli.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getNset.cc -o getNset.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hyperplan.cc -o hyperplan.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c initNerror.cc -o initNerror.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kleinkram.cc -o kleinkram.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c metropolis.cc -o metropolis.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nugget.cc -o nugget.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c operator.cc -o operator.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plusmalS.cc -o plusmalS.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rf_interfaces.cc -o rf_interfaces.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sequential.cc -o sequential.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spectral.cc -o spectral.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c startGetNset.cc -o startGetNset.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tbm.cc -o tbm.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trend.cc -o trend.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c userinterfaces.cc -o userinterfaces.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c variogramAndCo.cc -o variogramAndCo.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zzz.c -o zzz.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RandomFields.so AutoRandomFields.o Brown.o Coordinate_systems.o D.H.o Gneiting.o Huetchen.o InternalCov.o KeyInfo.o MLE.o PoissonPolygon.o Primitive.o QMath.o Specific.o SpherModels.o SpherModelsInitNerror.o Xempvario.o auxiliary.o avltr_modified.o circulant.o convhull2D.o cubicsolver.o direct.o empvario.o extremes.o families.o fft.o fftVario.o gauss.o gausslikeli.o getNset.o hyperplan.o initNerror.o kleinkram.o metropolis.o nugget.o operator.o plusmalS.o rf_interfaces.o sequential.o spectral.o startGetNset.o tbm.o trend.o userinterfaces.o variogramAndCo.o zzz.o -fopenmp -L/usr/local/lib/R/lib -lRlapack -lblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RandomFields/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (RandomFields) * installing *source* package ‘geoR’ ... ** package ‘geoR’ successfully unpacked and MD5 sums checked ** libs gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c geoR.c -o geoR.o gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o geoR.so geoR.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/geoR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Error : .onLoad failed in loadNamespace() for 'tcltk', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/usr/local/lib/R/library/tcltk/libs/tcltk.so': libtcl8.6.so: cannot open shared object file: No such file or directory ERROR: lazy loading failed for package ‘geoR’ * removing ‘/usr/local/lib/R/site-library/geoR’ The downloaded source packages are in ‘/tmp/downloaded_packages’ Warning message: In install.packages(pkgs, ...) : installation of package ‘geoR’ had non-zero exit status root@843af006d51b:/# root@843af006d51b:/# R R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(tcltk) Error: package or namespace load failed for ‘tcltk’: .onLoad failed in loadNamespace() for 'tcltk', details: call: dyn.load(file, DLLpath = DLLpath, ...) error: unable to load shared object '/usr/local/lib/R/library/tcltk/libs/tcltk.so': libtcl8.6.so: cannot open shared object file: No such file or directory > > root@843af006d51b:/# install2.r tcltk Warning messages: 1: package ‘tcltk’ is not available (for R version 3.5.2) 2: package ‘tcltk’ is a base package, and should not be updated root@843af006d51b:/# cd /usr/local/lib/R/library/tcltk/libs/ root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# cd .. root@843af006d51b:/usr/local/lib/R/library/tcltk# ls demo DESCRIPTION exec help html INDEX libs Meta NAMESPACE R root@843af006d51b:/usr/local/lib/R/library/tcltk# more DESCRIPTION Package: tcltk Version: 3.5.2 Priority: base Title: Tcl/Tk Interface Author: R Core Team Maintainer: R Core Team Description: Interface and language bindings to Tcl/Tk GUI elements. License: Part of R 3.5.2 Imports: utils NeedsCompilation: yes Built: R 3.5.2; x86_64-pc-linux-gnu; 2019-01-31 06:25:52 UTC; unix root@843af006d51b:/usr/local/lib/R/library/tcltk# cd libs/ root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# ls -la total 268 drwxr-sr-x 2 root staff 4096 Jan 31 06:36 . drwxr-sr-x 9 root staff 4096 Jan 31 06:36 .. -rwxr-xr-x 1 root staff 262744 Jan 31 06:36 tcltk.so root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# ldd tcltk.so linux-vdso.so.1 (0x00007ffeadbcc000) libtcl8.6.so => not found libtk8.6.so => not found libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f2cf852b000) libXss.so.1 => not found libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f2cf8319000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f2cf8015000) libR.so => not found libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f2cf7c76000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f2cf7a4e000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f2cf784a000) /lib64/ld-linux-x86-64.so.2 (0x00007f2cf8a74000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f2cf7646000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f2cf7440000) libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007f2cf722a000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f2cf7022000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f2cf6e05000) root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# apt-get install libtcl Reading package lists... Done Building dependency tree Reading state information... Done Package libtcl is a virtual package provided by: libtcl8.6 8.6.6+dfsg-1+b1 libtcl8.5 8.5.19-2+b1 You should explicitly select one to install. E: Package 'libtcl' has no installation candidate root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# apt-get install libtcl8.6 libtk8.6 Reading package lists... Done Building dependency tree Reading state information... Done The following additional packages will be installed: libxft2 libxss1 Suggested packages: tcl8.6 tk8.6 The following NEW packages will be installed: libtcl8.6 libtk8.6 libxft2 libxss1 0 upgraded, 4 newly installed, 0 to remove and 1 not upgraded. Need to get 1,813 kB of archives. After this operation, 6,715 kB of additional disk space will be used. Do you want to continue? [Y/n] y Get:1 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libxss1 amd64 1:1.2.2-1 [17.5 kB] Get:2 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libtcl8.6 amd64 8.6.6+dfsg-1+b1 [985 kB] Get:3 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:4 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libtk8.6 amd64 8.6.6-1+b1 [754 kB] Fetched 1,813 kB in 0s (3,117 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libxss1:amd64. (Reading database ... 22439 files and directories currently installed.) Preparing to unpack .../libxss1_1%3a1.2.2-1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.2-1) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../libtcl8.6_8.6.6+dfsg-1+b1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../libxft2_2.3.2-1+b2_amd64.deb ... Unpacking libxft2:amd64 (2.3.2-1+b2) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../libtk8.6_8.6.6-1+b1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.6-1+b1) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Processing triggers for libc-bin (2.24-11+deb9u3) ... Setting up libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Setting up libxft2:amd64 (2.3.2-1+b2) ... Setting up libtk8.6:amd64 (8.6.6-1+b1) ... Processing triggers for libc-bin (2.24-11+deb9u3) ... root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# apt- apt-cache apt-cdrom apt-config apt-get apt-key apt-mark root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# ldd tcltk.so linux-vdso.so.1 (0x00007ffdf99af000) libtcl8.6.so => /usr/lib/x86_64-linux-gnu/libtcl8.6.so (0x00007f6b52016000) libtk8.6.so => /usr/lib/x86_64-linux-gnu/libtk8.6.so (0x00007f6b51cb4000) libX11.so.6 => /usr/lib/x86_64-linux-gnu/libX11.so.6 (0x00007f6b51974000) libXss.so.1 => /usr/lib/x86_64-linux-gnu/libXss.so.1 (0x00007f6b51771000) libXext.so.6 => /usr/lib/x86_64-linux-gnu/libXext.so.6 (0x00007f6b5155f000) libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6b5125b000) libR.so => not found libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6b50ebc000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6b50cb8000) libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007f6b50a9e000) libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f6b50881000) libXft.so.2 => /usr/lib/x86_64-linux-gnu/libXft.so.2 (0x00007f6b5066b000) libfontconfig.so.1 => /usr/lib/x86_64-linux-gnu/libfontconfig.so.1 (0x00007f6b5042d000) libfreetype.so.6 => /usr/lib/x86_64-linux-gnu/libfreetype.so.6 (0x00007f6b5017e000) libxcb.so.1 => /usr/lib/x86_64-linux-gnu/libxcb.so.1 (0x00007f6b4ff56000) /lib64/ld-linux-x86-64.so.2 (0x00007f6b525d6000) libXrender.so.1 => /usr/lib/x86_64-linux-gnu/libXrender.so.1 (0x00007f6b4fd4c000) libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00007f6b4fb22000) libpng16.so.16 => /usr/lib/x86_64-linux-gnu/libpng16.so.16 (0x00007f6b4f8ef000) libXau.so.6 => /usr/lib/x86_64-linux-gnu/libXau.so.6 (0x00007f6b4f6eb000) libXdmcp.so.6 => /usr/lib/x86_64-linux-gnu/libXdmcp.so.6 (0x00007f6b4f4e5000) libbsd.so.0 => /lib/x86_64-linux-gnu/libbsd.so.0 (0x00007f6b4f2cf000) librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f6b4f0c7000) root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# R R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(tktcl + ) Error in library(tktcl) : there is no package called ‘tktcl’ > library(tcltk) Warning message: no DISPLAY variable so Tk is not available > root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# install2.r geoR trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/geoR_1.7-5.2.1.tar.gz' Content type 'application/octet-stream' length 413766 bytes (404 KB) ================================================== downloaded 404 KB * installing *source* package ‘geoR’ ... ** package ‘geoR’ successfully unpacked and MD5 sums checked ** libs gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c geoR.c -o geoR.o gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o geoR.so geoR.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/geoR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: no DISPLAY variable so Tk is not available ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Warning: no DISPLAY variable so Tk is not available * DONE (geoR) The downloaded source packages are in ‘/tmp/downloaded_packages’ root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# R R version 3.5.2 (2018-12-20) -- "Eggshell Igloo" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(spBayes) Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula > > root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# exitr bash: exitr: command not found root@843af006d51b:/usr/local/lib/R/library/tcltk/libs# exit exit lsrundel@tbBook [gp_pm25]$ ls analysis.R data docker gp_pm25.Rproj results rundel@tbBook [gp_pm25]$ rm -r results/ rundel@tbBook [gp_pm25]$ Rscript analysis.R Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) ---------------------------------------- General model description ---------------------------------------- Model fit with 110 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- Batch: 100 of 1000, 10.00% parameter acceptance tuning sigma.sq 64.0 0.85960 tau.sq 42.0 0.36375 phi 78.0 0.85960 ------------------------------------------------- Batch: 200 of 1000, 20.00% parameter acceptance tuning sigma.sq 48.0 1.53527 tau.sq 36.0 0.37110 phi 58.0 2.33662 ------------------------------------------------- Batch: 300 of 1000, 30.00% parameter acceptance tuning sigma.sq 48.0 1.50487 tau.sq 50.0 0.35655 phi 44.0 4.17330 ------------------------------------------------- Batch: 400 of 1000, 40.00% parameter acceptance tuning sigma.sq 34.0 1.47507 tau.sq 36.0 0.34257 phi 42.0 4.25761 ------------------------------------------------- Batch: 500 of 1000, 50.00% parameter acceptance tuning sigma.sq 38.0 1.50487 tau.sq 46.0 0.34949 phi 44.0 4.00966 ------------------------------------------------- Batch: 600 of 1000, 60.00% parameter acceptance tuning sigma.sq 36.0 1.50487 tau.sq 40.0 0.35655 phi 52.0 4.17330 ------------------------------------------------- Batch: 700 of 1000, 70.00% parameter acceptance tuning sigma.sq 34.0 1.50487 tau.sq 56.0 0.35655 phi 44.0 4.09066 ------------------------------------------------- Batch: 800 of 1000, 80.00% parameter acceptance tuning sigma.sq 44.0 1.50487 tau.sq 44.0 0.35655 phi 42.0 4.43136 ------------------------------------------------- Batch: 900 of 1000, 90.00% parameter acceptance tuning sigma.sq 46.0 1.44586 tau.sq 46.0 0.39404 phi 54.0 4.34362 ------------------------------------------------- Batch: 1000 of 1000, 100.00% parameter acceptance tuning sigma.sq 42.0 1.53527 tau.sq 56.0 0.36375 phi 48.0 4.17330 ------------------------------------------------- ---------------------------------------- General model description ---------------------------------------- Model fit with 110 observations. Prediction at 365 locations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. ------------------------------------------------- Sampling ------------------------------------------------- Sampled: 100 of 2500, 3.96% Sampled: 200 of 2500, 7.96% Sampled: 300 of 2500, 11.96% Sampled: 400 of 2500, 15.96% Sampled: 500 of 2500, 19.96% Sampled: 600 of 2500, 23.96% Sampled: 700 of 2500, 27.96% Sampled: 800 of 2500, 31.96% Sampled: 900 of 2500, 35.96% Sampled: 1000 of 2500, 39.96% Sampled: 1100 of 2500, 43.96% Sampled: 1200 of 2500, 47.96% Sampled: 1300 of 2500, 51.96% Sampled: 1400 of 2500, 55.96% Sampled: 1500 of 2500, 59.96% Sampled: 1600 of 2500, 63.96% Sampled: 1700 of 2500, 67.96% Sampled: 1800 of 2500, 71.96% Sampled: 1900 of 2500, 75.96% Sampled: 2000 of 2500, 79.96% Sampled: 2100 of 2500, 83.96% Sampled: 2200 of 2500, 87.96% Sampled: 2300 of 2500, 91.96% Sampled: 2400 of 2500, 95.96% Sampled: 2500 of 2500, 99.96% rundel@tbBook [gp_pm25]$ ls analysis.R data docker gp_pm25.Rproj results rundel@tbBook [gp_pm25]$ mkdir work rundel@tbBook [gp_pm25]$ ls analysis.R data docker gp_pm25.Rproj results work rundel@tbBook [gp_pm25]$ rm -fr work/ rundel@tbBook [gp_pm25]$ docker build --rm -t rundel/ex_pm25 docker/ Sending build context to Docker daemon 2.048kB Step 1/4 : FROM rocker/tidyverse:2.5.2 manifest for rocker/tidyverse:2.5.2 not found rundel@tbBook [gp_pm25]$ docker build --rm -t rundel/ex_pm25 docker/ Sending build context to Docker daemon 2.048kB Step 1/4 : FROM rocker/tidyverse:3.5.2 ---> 61266dee5826 Step 2/4 : RUN apt-get -y install libtcl8.6 libtk8.6 && install2.r --deps TRUE spBayes && mkdir /work ---> Running in 422f70d37c49 Reading package lists... Building dependency tree... Reading state information... The following additional packages will be installed: libxft2 libxss1 Suggested packages: tcl8.6 tk8.6 The following NEW packages will be installed: libtcl8.6 libtk8.6 libxft2 libxss1 0 upgraded, 4 newly installed, 0 to remove and 1 not upgraded. Need to get 1,813 kB of archives. After this operation, 6,715 kB of additional disk space will be used. Get:1 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libxss1 amd64 1:1.2.2-1 [17.5 kB] Get:2 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libtcl8.6 amd64 8.6.6+dfsg-1+b1 [985 kB] Get:3 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libxft2 amd64 2.3.2-1+b2 [56.5 kB] Get:4 http://cdn-fastly.deb.debian.org/debian stretch/main amd64 libtk8.6 amd64 8.6.6-1+b1 [754 kB] debconf: delaying package configuration, since apt-utils is not installed Fetched 1,813 kB in 0s (2,804 kB/s) Selecting previously unselected package libxss1:amd64. (Reading database ... 22439 files and directories currently installed.) Preparing to unpack .../libxss1_1%3a1.2.2-1_amd64.deb ... Unpacking libxss1:amd64 (1:1.2.2-1) ... Selecting previously unselected package libtcl8.6:amd64. Preparing to unpack .../libtcl8.6_8.6.6+dfsg-1+b1_amd64.deb ... Unpacking libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Selecting previously unselected package libxft2:amd64. Preparing to unpack .../libxft2_2.3.2-1+b2_amd64.deb ... Unpacking libxft2:amd64 (2.3.2-1+b2) ... Selecting previously unselected package libtk8.6:amd64. Preparing to unpack .../libtk8.6_8.6.6-1+b1_amd64.deb ... Unpacking libtk8.6:amd64 (8.6.6-1+b1) ... Setting up libxss1:amd64 (1:1.2.2-1) ... Processing triggers for libc-bin (2.24-11+deb9u3) ... Setting up libtcl8.6:amd64 (8.6.6+dfsg-1+b1) ... Setting up libxft2:amd64 (2.3.2-1+b2) ... Setting up libtk8.6:amd64 (8.6.6-1+b1) ... Processing triggers for libc-bin (2.24-11+deb9u3) ... also installing the dependencies ‘RandomFieldsUtils’, ‘sp’, ‘splancs’, ‘RandomFields’, ‘coda’, ‘magic’, ‘abind’, ‘Formula’, ‘MBA’, ‘geoR’ trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/RandomFieldsUtils_0.3.25.tar.gz' Content type 'application/octet-stream' length 111100 bytes (108 KB) ================================================== downloaded 108 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/sp_1.3-1.tar.gz' Content type 'application/octet-stream' length 1133621 bytes (1.1 MB) ================================================== downloaded 1.1 MB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/splancs_2.01-40.tar.gz' Content type 'application/octet-stream' length 105583 bytes (103 KB) ================================================== downloaded 103 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/RandomFields_3.1.50.tar.gz' Content type 'application/octet-stream' length 1783992 bytes (1.7 MB) ================================================== downloaded 1.7 MB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/coda_0.19-2.tar.gz' Content type 'application/octet-stream' length 73530 bytes (71 KB) ================================================== downloaded 71 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/magic_1.5-9.tar.gz' Content type 'application/octet-stream' length 150612 bytes (147 KB) ================================================== downloaded 147 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/abind_1.4-5.tar.gz' Content type 'application/octet-stream' length 21810 bytes (21 KB) ================================================== downloaded 21 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/Formula_1.2-3.tar.gz' Content type 'application/octet-stream' length 151340 bytes (147 KB) ================================================== downloaded 147 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/MBA_0.0-9.tar.gz' Content type 'application/octet-stream' length 140993 bytes (137 KB) ================================================== downloaded 137 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/geoR_1.7-5.2.1.tar.gz' Content type 'application/octet-stream' length 413766 bytes (404 KB) ================================================== downloaded 404 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/spBayes_0.4-1.tar.gz' Content type 'application/octet-stream' length 496081 bytes (484 KB) ================================================== downloaded 484 KB * installing *source* package ‘RandomFieldsUtils’ ... ** package ‘RandomFieldsUtils’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RFoptions.cc -o RFoptions.o f95 -fpic -g -O2 -c bckslvmodified.f -o bckslvmodified.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c brdomain.cc -o brdomain.o f95 -fpic -g -O2 -c cholmodified.f -o cholmodified.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c diffusion.cc -o diffusion.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init_RandomFieldsUtils.c -o init_RandomFieldsUtils.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kleinkram.cc -o kleinkram.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c maths.cc -o maths.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c options.cc -o options.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c own.cc -o own.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c scalar.cc -o scalar.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c solve.cc -o solve.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sort.cc -o sort.o f95 -fpic -g -O2 -c spamown.f -o spamown.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c utils.cc -o utils.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c win_linux_aux.cc -o win_linux_aux.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RandomFieldsUtils.so RFoptions.o bckslvmodified.o brdomain.o cholmodified.o diffusion.o init_RandomFieldsUtils.o kleinkram.o maths.o options.o own.o scalar.o solve.o sort.o spamown.o utils.o win_linux_aux.o -fopenmp -L/usr/local/lib/R/lib -lRlapack -lblas -lgfortran -lm -lquadmath -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RandomFieldsUtils/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (RandomFieldsUtils) * installing *source* package ‘sp’ ... ** package ‘sp’ successfully unpacked and MD5 sums checked ** libs gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rcentroid.c -o Rcentroid.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gcdist.c -o gcdist.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pip.c -o pip.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c pip2.c -o pip2.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sp_xports.c -o sp_xports.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c surfaceArea.c -o surfaceArea.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zerodist.c -o zerodist.o gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o sp.so Rcentroid.o gcdist.o init.o pip.o pip2.o sp_xports.o surfaceArea.o zerodist.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/sp/libs ** R ** data ** demo ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (sp) * installing *source* package ‘coda’ ... ** package ‘coda’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (coda) * installing *source* package ‘abind’ ... ** package ‘abind’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (abind) * installing *source* package ‘Formula’ ... ** package ‘Formula’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (Formula) * installing *source* package ‘MBA’ ... ** package ‘MBA’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MBA.cpp -o MBA.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBA.cpp:50: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MBAPoints.cpp -o MBAPoints.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBAPoints.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MBASurf.cpp -o MBASurf.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from include/MBA.h:39, from MBASurf.cpp:1: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MBAdata.cpp -o MBAdata.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/MBAdata.h:38, from MBAdata.cpp:35: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c UCBsplineSurface.cpp -o UCBsplineSurface.o In file included from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:28:0, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/detail/shared_count.hpp:355:33: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_count( std::auto_ptr & r ): pi_( new sp_counted_impl_p( r.get() ) ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:256:65: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R > ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:471:31: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] explicit shared_ptr( std::auto_ptr & r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:484:22: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr( std::auto_ptr && r ): px(r.get()), pn() ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:567:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr & r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:576:34: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] shared_ptr & operator=( std::auto_ptr && r ) ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ In file included from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17:0, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr& boost::shared_ptr::operator=(std::auto_ptr<_Up>&&)’: /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:578:38: warning: ‘template class std::auto_ptr’ is deprecated [-Wdeprecated-declarations] this_type( static_cast< std::auto_ptr && >( r ) ).swap( *this ); ^~~~~~~~ In file included from /usr/include/c++/6/memory:81:0, from /usr/local/lib/R/site-library/BH/include/boost/config/no_tr1/memory.hpp:21, from /usr/local/lib/R/site-library/BH/include/boost/smart_ptr/shared_ptr.hpp:23, from /usr/local/lib/R/site-library/BH/include/boost/shared_ptr.hpp:17, from include/UCBsplineSurface.h:36, from UCBsplineSurface.cpp:36: /usr/include/c++/6/bits/unique_ptr.h:49:28: note: declared here template class auto_ptr; ^~~~~~~~ g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c UCBsplines.cpp -o UCBsplines.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o MBA.so MBA.o MBAPoints.o MBASurf.o MBAdata.o UCBsplineSurface.o UCBsplines.o init.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/MBA/libs ** R ** data ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (MBA) * installing *source* package ‘splancs’ ... ** package ‘splancs’ successfully unpacked and MD5 sums checked ** libs f95 -fpic -g -O2 -c areapl.f -o areapl.o f95 -fpic -g -O2 -c cncvwt.f -o cncvwt.o f95 -fpic -g -O2 -c dokhat.f -o dokhat.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o f95 -fpic -g -O2 -c inpip.f -o inpip.o f95 -fpic -g -O2 -c ipippa.f -o ipippa.o f95 -fpic -g -O2 -c iplace.f -o iplace.o f95 -fpic -g -O2 -c k12hat.f -o k12hat.o f95 -fpic -g -O2 -c kernel3d.f -o kernel3d.o f95 -fpic -g -O2 -c khvc.f -o khvc.o f95 -fpic -g -O2 -c khvmat.f -o khvmat.o f95 -fpic -g -O2 -c krnnrm.f -o krnnrm.o f95 -fpic -g -O2 -c krnqne.f -o krnqne.o f95 -fpic -g -O2 -c krnqrt.f -o krnqrt.o f95 -fpic -g -O2 -c nndist.f -o nndist.o f95 -fpic -g -O2 -c plarea.f -o plarea.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptinpoly.c -o ptinpoly.o f95 -fpic -g -O2 -c sekhat.f -o sekhat.o f95 -fpic -g -O2 -c sort.f -o sort.o f95 -fpic -g -O2 -c sort2.f -o sort2.o f95 -fpic -g -O2 -c stkhat.f -o stkhat.o f95 -fpic -g -O2 -c stsecal.f -o stsecal.o f95 -fpic -g -O2 -c tribble.f -o tribble.o f95 -fpic -g -O2 -c twodimmse.f -o twodimmse.o f95 -fpic -g -O2 -c weight.f -o weight.o gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o splancs.so areapl.o cncvwt.o dokhat.o init.o inpip.o ipippa.o iplace.o k12hat.o kernel3d.o khvc.o khvmat.o krnnrm.o krnqne.o krnqrt.o nndist.o plarea.o ptinpoly.o sekhat.o sort.o sort2.o stkhat.o stsecal.o tribble.o twodimmse.o weight.o -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/splancs/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (splancs) * installing *source* package ‘RandomFields’ ... ** package ‘RandomFields’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c AutoRandomFields.cc -o AutoRandomFields.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Brown.cc -o Brown.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Coordinate_systems.cc -o Coordinate_systems.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c D.H.cc -o D.H.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Gneiting.cc -o Gneiting.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Huetchen.cc -o Huetchen.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c InternalCov.cc -o InternalCov.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c KeyInfo.cc -o KeyInfo.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MLE.cc -o MLE.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c PoissonPolygon.cc -o PoissonPolygon.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Primitive.cc -o Primitive.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c QMath.cc -o QMath.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Specific.cc -o Specific.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SpherModels.cc -o SpherModels.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c SpherModelsInitNerror.cc -o SpherModelsInitNerror.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Xempvario.cc -o Xempvario.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c auxiliary.cc -o auxiliary.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c avltr_modified.cc -o avltr_modified.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c circulant.cc -o circulant.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c convhull2D.cc -o convhull2D.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c cubicsolver.cc -o cubicsolver.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c direct.cc -o direct.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c empvario.cc -o empvario.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c extremes.cc -o extremes.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c families.cc -o families.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fft.c -o fft.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fftVario.cc -o fftVario.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gauss.cc -o gauss.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gausslikeli.cc -o gausslikeli.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c getNset.cc -o getNset.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c hyperplan.cc -o hyperplan.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c initNerror.cc -o initNerror.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c kleinkram.cc -o kleinkram.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c metropolis.cc -o metropolis.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nugget.cc -o nugget.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c operator.cc -o operator.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c plusmalS.cc -o plusmalS.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rf_interfaces.cc -o rf_interfaces.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c sequential.cc -o sequential.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spectral.cc -o spectral.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c startGetNset.cc -o startGetNset.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c tbm.cc -o tbm.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trend.cc -o trend.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c userinterfaces.cc -o userinterfaces.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fopenmp -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c variogramAndCo.cc -o variogramAndCo.o gcc -I"/usr/local/lib/R/include" -DNDEBUG -I"/usr/local/lib/R/site-library/RandomFieldsUtils/include" -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c zzz.c -o zzz.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RandomFields.so AutoRandomFields.o Brown.o Coordinate_systems.o D.H.o Gneiting.o Huetchen.o InternalCov.o KeyInfo.o MLE.o PoissonPolygon.o Primitive.o QMath.o Specific.o SpherModels.o SpherModelsInitNerror.o Xempvario.o auxiliary.o avltr_modified.o circulant.o convhull2D.o cubicsolver.o direct.o empvario.o extremes.o families.o fft.o fftVario.o gauss.o gausslikeli.o getNset.o hyperplan.o initNerror.o kleinkram.o metropolis.o nugget.o operator.o plusmalS.o rf_interfaces.o sequential.o spectral.o startGetNset.o tbm.o trend.o userinterfaces.o variogramAndCo.o zzz.o -fopenmp -L/usr/local/lib/R/lib -lRlapack -lblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/RandomFields/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (RandomFields) * installing *source* package ‘magic’ ... ** package ‘magic’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (magic) * installing *source* package ‘geoR’ ... ** package ‘geoR’ successfully unpacked and MD5 sums checked ** libs gcc -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c geoR.c -o geoR.o gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o geoR.so geoR.o -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/geoR/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: no DISPLAY variable so Tk is not available ** help *** installing help indices ** building package indices ** testing if installed package can be loaded Warning: no DISPLAY variable so Tk is not available * DONE (geoR) * installing *source* package ‘spBayes’ ... ** package ‘spBayes’ successfully unpacked and MD5 sums checked ** libs g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c adaptMetropGibbs.cpp -o adaptMetropGibbs.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c idist.cpp -o idist.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.cpp -o init.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c mkSpCov.cpp -o mkSpCov.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nonSpGLM_AMCMC.cpp -o nonSpGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ptsInPoly.cpp -o ptsInPoly.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spDynLM.cpp -o spDynLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spGLM.cpp -o spGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spGLM_AMCMC.cpp -o spGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLM.cpp -o spLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLMPredict.cpp -o spLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spLMRecover.cpp -o spLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMPPMvDIC.cpp -o spMPPMvDIC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalign.cpp -o spMisalign.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignGLM.cpp -o spMisalignGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignGLMPredict.cpp -o spMisalignGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignPredict.cpp -o spMisalignPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMisalignRecover.cpp -o spMisalignRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLM.cpp -o spMvGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLMPredict.cpp -o spMvGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvGLM_AMCMC.cpp -o spMvGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLM.cpp -o spMvLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLMPredict.cpp -o spMvLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spMvLMRecover.cpp -o spMvLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPDynLM.cpp -o spPPDynLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPGLM.cpp -o spPPGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPGLM_AMCMC.cpp -o spPPGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLM.cpp -o spPPLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLMPredict.cpp -o spPPLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPLMRecover.cpp -o spPPLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLM.cpp -o spPPMvGLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLMPredict.cpp -o spPPMvGLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvGLM_AMCMC.cpp -o spPPMvGLM_AMCMC.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLM.cpp -o spPPMvLM.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLMPredict.cpp -o spPPMvLMPredict.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spPPMvLMRecover.cpp -o spPPMvLMRecover.o g++ -I"/usr/local/lib/R/include" -DNDEBUG -I/usr/local/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c util.cpp -o util.o g++ -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o spBayes.so adaptMetropGibbs.o idist.o init.o mkSpCov.o nonSpGLM_AMCMC.o ptsInPoly.o spDynLM.o spGLM.o spGLM_AMCMC.o spLM.o spLMPredict.o spLMRecover.o spMPPMvDIC.o spMisalign.o spMisalignGLM.o spMisalignGLMPredict.o spMisalignPredict.o spMisalignRecover.o spMvGLM.o spMvGLMPredict.o spMvGLM_AMCMC.o spMvLM.o spMvLMPredict.o spMvLMRecover.o spPPDynLM.o spPPGLM.o spPPGLM_AMCMC.o spPPLM.o spPPLMPredict.o spPPLMRecover.o spPPMvGLM.o spPPMvGLMPredict.o spPPMvGLM_AMCMC.o spPPMvLM.o spPPMvLMPredict.o spPPMvLMRecover.o util.o -L/usr/local/lib/R/lib -lRlapack -lblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR installing to /usr/local/lib/R/site-library/spBayes/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (spBayes) The downloaded source packages are in ‘/tmp/downloaded_packages’ Removing intermediate container 422f70d37c49 ---> 924ff7bd6b25 Step 3/4 : WORKDIR /work ---> Running in f1436aff3eaa Removing intermediate container f1436aff3eaa ---> 0faee76748dd Step 4/4 : ENTRYPOINT ["Rscript"] ---> Running in fab6f4fc1160 Removing intermediate container fab6f4fc1160 ---> e960520e38c3 Successfully built e960520e38c3 Successfully tagged rundel/ex_pm25:latest rundel@tbBook [gp_pm25]$ rundel@tbBook [gp_pm25]$ docker build --rm -t rundel/ex_pm25_tidy -f docker/Dockerfile_tidybayes "docker build" requires exactly 1 argument. See 'docker build --help'. Usage: docker build [OPTIONS] PATH | URL | - Build an image from a Dockerfile rundel@tbBook [gp_pm25]$ docker build --rm -t rundel/ex_pm25_tidy docker/Dockerfile_tidybayes unable to prepare context: context must be a directory: /Users/rundel/Desktop/Sta790/Resources/gp_pm25/docker/Dockerfile_tidybayes rundel@tbBook [gp_pm25]$ docker build --rm -t rundel/ex_pm25_tidy -f Dockerfile_tidybayes docker/ unable to prepare context: unable to evaluate symlinks in Dockerfile path: lstat /Users/rundel/Desktop/Sta790/Resources/gp_pm25/Dockerfile_tidybayes: no such file or directory rundel@tbBook [gp_pm25]$ docker build --rm -t rundel/ex_pm25_tidy -f docker/Dockerfile_tidybayes docker/ Sending build context to Docker daemon 3.072kB Step 1/2 : FROM rundel/ex_pm25 ---> e960520e38c3 Step 2/2 : RUN install2.r tidybayes ---> Running in 1bfd2197fc93 also installing the dependencies ‘svUnit’, ‘LaplacesDemon’, ‘ggstance’, ‘ggridges’, ‘HDInterval’, ‘arrayhelpers’ trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/svUnit_0.7-12.tar.gz' Content type 'application/octet-stream' length 1003986 bytes (980 KB) ================================================== downloaded 980 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/LaplacesDemon_16.1.1.tar.gz' Content type 'application/octet-stream' length 2801708 bytes (2.7 MB) ================================================== downloaded 2.7 MB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/ggstance_0.3.1.tar.gz' Content type 'application/octet-stream' length 127106 bytes (124 KB) ================================================== downloaded 124 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/ggridges_0.5.1.tar.gz' Content type 'application/octet-stream' length 1986894 bytes (1.9 MB) ================================================== downloaded 1.9 MB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/HDInterval_0.2.0.tar.gz' Content type 'application/octet-stream' length 28147 bytes (27 KB) ================================================== downloaded 27 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/arrayhelpers_1.0-20160527.tar.gz' Content type 'application/octet-stream' length 19339 bytes (18 KB) ================================================== downloaded 18 KB trying URL 'https://mran.microsoft.com/snapshot/2019-01-30/src/contrib/tidybayes_1.0.3.tar.gz' Content type 'application/octet-stream' length 1631807 bytes (1.6 MB) ================================================== downloaded 1.6 MB * installing *source* package ‘svUnit’ ... ** package ‘svUnit’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (svUnit) * installing *source* package ‘LaplacesDemon’ ... ** package ‘LaplacesDemon’ successfully unpacked and MD5 sums checked ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (LaplacesDemon) * installing *source* package ‘ggstance’ ... ** package ‘ggstance’ successfully unpacked and MD5 sums checked ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (ggstance) * installing *source* package ‘ggridges’ ... ** package ‘ggridges’ successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (ggridges) * installing *source* package ‘HDInterval’ ... ** package ‘HDInterval’ successfully unpacked and MD5 sums checked ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** testing if installed package can be loaded * DONE (HDInterval) * installing *source* package ‘arrayhelpers’ ... ** package ‘arrayhelpers’ successfully unpacked and MD5 sums checked ** R ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** testing if installed package can be loaded * DONE (arrayhelpers) * installing *source* package ‘tidybayes’ ... ** package ‘tidybayes’ successfully unpacked and MD5 sums checked ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (tidybayes) The downloaded source packages are in ‘/tmp/downloaded_packages’ Removing intermediate container 1bfd2197fc93 ---> 7579cad66121 Successfully built 7579cad66121 Successfully tagged rundel/ex_pm25_tidy:latest rundel@tbBook [gp_pm25]$ rundel@tbBook [gp_pm25]$ ls analysis.R data docker gp_pm25.Rproj results rundel@tbBook [gp_pm25]$ docker images REPOSITORY TAG IMAGE ID CREATED SIZE rundel/ex_pm25_tidy latest 7579cad66121 23 seconds ago 1.91GB rundel/ex_pm25 latest e960520e38c3 3 minutes ago 1.89GB rocker/tidyverse 3.5.2 61266dee5826 9 hours ago 1.86GB rocker/tidyverse latest 61266dee5826 9 hours ago 1.86GB ubuntu 18.10 88fdd57278f5 8 days ago 73.7MB rundel@tbBook [gp_pm25]$ rm -r results/ rundel@tbBook [gp_pm25]$ docker run --rm rundel/ex_pm25 analysis.R Fatal error: cannot open file 'analysis.R': No such file or directory rundel@tbBook [gp_pm25]$ ls analysis.R data docker gp_pm25.Rproj rundel@tbBook [gp_pm25]$ docker run --rm rundel/ex_pm25 ./analysis.R Fatal error: cannot open file './analysis.R': No such file or directory rundel@tbBook [gp_pm25]$ docker run --rm -it rundel/ex_pm25 /bin/bash Error: unexpected input in "" Execution halted rundel@tbBook [gp_pm25]$ Rscript /bin/bash Error: invalid multibyte character in parser at line 1 Error: EOF whilst reading MBCS char at line 1 Error: EOF whilst reading MBCS char at line 1 Error: invalid multibyte character in parser at line 1 rundel@tbBook [gp_pm25]$ docker run --rm -it --entrypoint /bin/bash rundel/ex_pm25 root@7dcc0a1ee649:/work# Rscript analysis.R Fatal error: cannot open file 'analysis.R': No such file or directory root@7dcc0a1ee649:/work# ls root@7dcc0a1ee649:/work# exit rundel@tbBook [gp_pm25]$ docker run --rm -it --entrypoint /bin/bash -v ./:/work rundel/ex_pm25 docker: Error response from daemon: create ./: "./" includes invalid characters for a local volume name, only "[a-zA-Z0-9][a-zA-Z0-9_.-]" are allowed. If you intended to pass a host directory, use absolute path. See 'docker run --help'. rundel@tbBook [gp_pm25]$ docker run --rm -it --entrypoint /bin/bash -v ~:/work rundel/ex_pm25 root@f49913261735:/work# ls Applications Books check_mdworker.sh crlcache2.db Documents Drive GoPro Library Music Public shiny.R Sites Blizzard Box Sync check_R.sh Desktop Downloads Dropbox iCloud Drive (Archive) Movies Pictures Scratch singularity-vm System root@f49913261735:/work# exit exit rundel@tbBook [gp_pm25]$ rundel@tbBook [gp_pm25]$ pwd /Users/rundel/Desktop/Sta790/Resources/gp_pm25 rundel@tbBook [gp_pm25]$ echo pwd pwd rundel@tbBook [gp_pm25]$ echo $(pwd) /Users/rundel/Desktop/Sta790/Resources/gp_pm25 rundel@tbBook [gp_pm25]$ pwd | echo rundel@tbBook [gp_pm25]$ pwd > echo rundel@tbBook [gp_pm25]$ ls analysis.R data docker echo gp_pm25.Rproj rundel@tbBook [gp_pm25]$ rm echo rundel@tbBook [gp_pm25]$ echo $(pwd) /Users/rundel/Desktop/Sta790/Resources/gp_pm25 rundel@tbBook [gp_pm25]$ echo `pwd` /Users/rundel/Desktop/Sta790/Resources/gp_pm25 rundel@tbBook [gp_pm25]$ docker run --rm -it --entrypoint /bin/bash -v $(pwd):/work rundel/ex_pm25 root@3c45b89af7f4:/work# ls analysis.R data docker gp_pm25.Rproj root@3c45b89af7f4:/work# Rscript analysis.R Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) ---------------------------------------- General model description ---------------------------------------- Model fit with 110 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- ^C Execution halted root@3c45b89af7f4:/work# exit exit rundel@tbBook [gp_pm25]$ docker run --rm -it -v $(pwd):/work rundel/ex_pm25 analysis.R Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) ---------------------------------------- General model description ---------------------------------------- Model fit with 110 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- Batch: 100 of 1000, 10.00% parameter acceptance tuning sigma.sq 54.0 0.85960 tau.sq 26.0 0.34949 phi 82.0 0.85960 ------------------------------------------------- Batch: 200 of 1000, 20.00% parameter acceptance tuning sigma.sq 42.0 1.50487 tau.sq 42.0 0.33578 phi 60.0 2.33662 ------------------------------------------------- Batch: 300 of 1000, 30.00% parameter acceptance tuning sigma.sq 40.0 1.56629 tau.sq 34.0 0.32913 phi 40.0 4.17330 ------------------------------------------------- Batch: 400 of 1000, 40.00% parameter acceptance tuning sigma.sq 42.0 1.53527 tau.sq 40.0 0.34949 phi 56.0 4.17330 ------------------------------------------------- Batch: 500 of 1000, 50.00% parameter acceptance tuning sigma.sq 50.0 1.66314 tau.sq 40.0 0.34949 phi 58.0 4.25761 ------------------------------------------------- Batch: 600 of 1000, 60.00% parameter acceptance tuning sigma.sq 38.0 1.53527 tau.sq 36.0 0.35655 phi 40.0 4.43136 ------------------------------------------------- Batch: 700 of 1000, 70.00% parameter acceptance tuning sigma.sq 30.0 1.50487 tau.sq 42.0 0.32913 phi 48.0 4.43136 ------------------------------------------------- Batch: 800 of 1000, 80.00% parameter acceptance tuning sigma.sq 34.0 1.47507 tau.sq 44.0 0.35655 phi 28.0 4.00966 ------------------------------------------------- Batch: 900 of 1000, 90.00% parameter acceptance tuning sigma.sq 42.0 1.53527 tau.sq 42.0 0.34949 phi 38.0 4.25761 ------------------------------------------------- Batch: 1000 of 1000, 100.00% parameter acceptance tuning sigma.sq 42.0 1.44586 tau.sq 40.0 0.36375 phi 54.0 4.09066 ------------------------------------------------- ---------------------------------------- General model description ---------------------------------------- Model fit with 110 observations. Prediction at 365 locations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. ------------------------------------------------- Sampling ------------------------------------------------- Sampled: 100 of 2500, 3.96% Sampled: 200 of 2500, 7.96% Sampled: 300 of 2500, 11.96% Sampled: 400 of 2500, 15.96% Sampled: 500 of 2500, 19.96% Sampled: 600 of 2500, 23.96% Sampled: 700 of 2500, 27.96% Sampled: 800 of 2500, 31.96% Sampled: 900 of 2500, 35.96% Sampled: 1000 of 2500, 39.96% Sampled: 1100 of 2500, 43.96% Sampled: 1200 of 2500, 47.96% Sampled: 1300 of 2500, 51.96% Sampled: 1400 of 2500, 55.96% Sampled: 1500 of 2500, 59.96% Sampled: 1600 of 2500, 63.96% Sampled: 1700 of 2500, 67.96% Sampled: 1800 of 2500, 71.96% Sampled: 1900 of 2500, 75.96% Sampled: 2000 of 2500, 79.96% Sampled: 2100 of 2500, 83.96% Sampled: 2200 of 2500, 87.96% Sampled: 2300 of 2500, 91.96% Sampled: 2400 of 2500, 95.96% Sampled: 2500 of 2500, 99.96% rundel@tbBook [gp_pm25]$ ls analysis.R data docker gp_pm25.Rproj results rundel@tbBook [gp_pm25]$ open results/ rundel@tbBook [gp_pm25]$ rundel@tbBook [gp_pm25]$ Rscript .DS_Store .git/ analysis.R data/ gp_pm25.Rproj .Rproj.user/ .gitignore command_args_demo.R docker/ results/ rundel@tbBook [gp_pm25]$ Rscript command_args_demo.R chr(0) NULL rundel@tbBook [gp_pm25]$ Rscript command_args_demo.R --arg 1 --blah --test -f chr [1:5] "--arg" "1" "--blah" "--test" "-f" NULL rundel@tbBook [gp_pm25]$ Rscript command_args_demo.R 1 ] chr "1" NULL rundel@tbBook [gp_pm25]$ Rscript command_args_demo.R 2 chr "2" NULL rundel@tbBook [gp_pm25]$ rundel@tbBook [gp_pm25]$ Rscript analysis.R 1 Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) rundel@tbBook [gp_pm25]$ Rscript analysis.R 1 1 2 Error: Provide only one index Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) rundel@tbBook [gp_pm25]$ Rscript analysis.R 1 1 2 Error: Provide only one index Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) rundel@tbBook [gp_pm25]$ Rscript analysis.R 1 1 2 Error: Provide only one index rundel@tbBook [gp_pm25]$ Rscript analysis.R 2 Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) ---------------------------------------- General model description ---------------------------------------- Model fit with 120 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- Batch: 100 of 1000, 10.00% parameter acceptance tuning sigma.sq 62.0 0.85960 tau.sq 32.0 0.35655 phi 84.0 0.85960 ------------------------------------------------- Batch: 200 of 1000, 20.00% parameter acceptance tuning sigma.sq 56.0 1.11484 tau.sq 40.0 0.34257 phi 70.0 2.33662 ------------------------------------------------- Batch: 300 of 1000, 30.00% parameter acceptance tuning sigma.sq 48.0 1.11484 tau.sq 42.0 0.36375 phi 46.0 4.09066 ------------------------------------------------- Batch: 400 of 1000, 40.00% parameter acceptance tuning sigma.sq 44.0 1.11484 tau.sq 56.0 0.32262 phi 44.0 4.09066 ------------------------------------------------- Batch: 500 of 1000, 50.00% parameter acceptance tuning sigma.sq 58.0 1.11484 tau.sq 44.0 0.35655 phi 38.0 4.00966 ------------------------------------------------- Batch: 600 of 1000, 60.00% parameter acceptance tuning sigma.sq 44.0 1.11484 tau.sq 48.0 0.35655 phi 36.0 4.17330 ------------------------------------------------- Batch: 700 of 1000, 70.00% parameter acceptance tuning sigma.sq 36.0 1.13736 tau.sq 34.0 0.35655 phi 28.0 4.52088 ------------------------------------------------- Batch: 800 of 1000, 80.00% parameter acceptance tuning sigma.sq 42.0 1.11484 tau.sq 42.0 0.36375 phi 52.0 4.17330 ------------------------------------------------- Batch: 900 of 1000, 90.00% parameter acceptance tuning sigma.sq 44.0 1.16033 tau.sq 42.0 0.34257 phi 44.0 4.25761 ------------------------------------------------- Batch: 1000 of 1000, 100.00% parameter acceptance tuning sigma.sq 52.0 1.13736 tau.sq 30.0 0.34949 phi 52.0 4.52088 ------------------------------------------------- ---------------------------------------- General model description ---------------------------------------- Model fit with 120 observations. Prediction at 365 locations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. ------------------------------------------------- Sampling ------------------------------------------------- Sampled: 100 of 2500, 3.96% Sampled: 200 of 2500, 7.96% Sampled: 300 of 2500, 11.96% Sampled: 400 of 2500, 15.96% Sampled: 500 of 2500, 19.96% Sampled: 600 of 2500, 23.96% Sampled: 700 of 2500, 27.96% Sampled: 800 of 2500, 31.96% Sampled: 900 of 2500, 35.96% Sampled: 1000 of 2500, 39.96% Sampled: 1100 of 2500, 43.96% Sampled: 1200 of 2500, 47.96% Sampled: 1300 of 2500, 51.96% Sampled: 1400 of 2500, 55.96% Sampled: 1500 of 2500, 59.96% Sampled: 1600 of 2500, 63.96% Sampled: 1700 of 2500, 67.96% Sampled: 1800 of 2500, 71.96% Sampled: 1900 of 2500, 75.96% Sampled: 2000 of 2500, 79.96% Sampled: 2100 of 2500, 83.96% Sampled: 2200 of 2500, 87.96% Sampled: 2300 of 2500, 91.96% Sampled: 2400 of 2500, 95.96% Sampled: 2500 of 2500, 99.96% null device 1 rundel@tbBook [gp_pm25]$ open results/ rundel@tbBook [gp_pm25]$ Rscript analysis.R Error: Provide only one index rundel@tbBook [gp_pm25]$ Rscript analysis.R A Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) Error: !is.na(site_index) is not TRUE In addition: Warning message: NAs introduced by coercion Backtrace: █ 1. └─base::stopifnot(!is.na(site_index)) rundel@tbBook [gp_pm25]$ Rscript analysis.R 0 Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) Error: site_index %in% seq_along(sites) is not TRUE Backtrace: █ 1. └─base::stopifnot(site_index %in% seq_along(sites)) rundel@tbBook [gp_pm25]$ Rscript analysis.R 1000 Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) Error: site_index %in% seq_along(sites) is not TRUE Backtrace: █ 1. └─base::stopifnot(site_index %in% seq_along(sites)) rundel@tbBook [gp_pm25]$ rundel@tbBook [gp_pm25]$ docker run --rm -it -v $(pwd):/work rundel/ex_pm25 analysis.R 3 Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) ---------------------------------------- General model description ---------------------------------------- Model fit with 116 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- Batch: 100 of 1000, 10.00% parameter acceptance tuning sigma.sq 50.0 0.84258 tau.sq 38.0 0.32262 phi 74.0 0.85960 ------------------------------------------------- Batch: 200 of 1000, 20.00% parameter acceptance tuning sigma.sq 28.0 1.20769 tau.sq 38.0 0.34257 phi 70.0 2.33662 ------------------------------------------------- Batch: 300 of 1000, 30.00% parameter acceptance tuning sigma.sq 44.0 1.16033 tau.sq 40.0 0.35655 phi 44.0 4.00966 ------------------------------------------------- Batch: 400 of 1000, 40.00% parameter acceptance tuning sigma.sq 42.0 1.23208 tau.sq 48.0 0.37859 phi 44.0 4.34362 ------------------------------------------------- Batch: 500 of 1000, 50.00% parameter acceptance tuning sigma.sq 30.0 1.18377 tau.sq 34.0 0.33578 phi 44.0 4.52088 ------------------------------------------------- Batch: 600 of 1000, 60.00% parameter acceptance tuning sigma.sq 42.0 1.23208 tau.sq 32.0 0.35655 phi 32.0 4.17330 ------------------------------------------------- Batch: 700 of 1000, 70.00% parameter acceptance tuning sigma.sq 40.0 1.16033 tau.sq 38.0 0.36375 phi 42.0 4.52088 ------------------------------------------------- Batch: 800 of 1000, 80.00% parameter acceptance tuning sigma.sq 40.0 1.09276 tau.sq 38.0 0.34257 phi 54.0 4.34362 ------------------------------------------------- Batch: 900 of 1000, 90.00% parameter acceptance tuning sigma.sq 32.0 1.09276 tau.sq 42.0 0.33578 phi 40.0 4.17330 ------------------------------------------------- Batch: 1000 of 1000, 100.00% parameter acceptance tuning sigma.sq 60.0 1.20769 tau.sq 42.0 0.34949 phi 48.0 4.34362 ------------------------------------------------- ---------------------------------------- General model description ---------------------------------------- Model fit with 116 observations. Prediction at 365 locations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. ------------------------------------------------- Sampling ------------------------------------------------- Sampled: 100 of 2500, 3.96% Sampled: 200 of 2500, 7.96% Sampled: 300 of 2500, 11.96% Sampled: 400 of 2500, 15.96% Sampled: 500 of 2500, 19.96% Sampled: 600 of 2500, 23.96% Sampled: 700 of 2500, 27.96% Sampled: 800 of 2500, 31.96% Sampled: 900 of 2500, 35.96% Sampled: 1000 of 2500, 39.96% Sampled: 1100 of 2500, 43.96% Sampled: 1200 of 2500, 47.96% Sampled: 1300 of 2500, 51.96% Sampled: 1400 of 2500, 55.96% Sampled: 1500 of 2500, 59.96% Sampled: 1600 of 2500, 63.96% Sampled: 1700 of 2500, 67.96% Sampled: 1800 of 2500, 71.96% Sampled: 1900 of 2500, 75.96% Sampled: 2000 of 2500, 79.96% Sampled: 2100 of 2500, 83.96% Sampled: 2200 of 2500, 87.96% Sampled: 2300 of 2500, 91.96% Sampled: 2400 of 2500, 95.96% Sampled: 2500 of 2500, 99.96% null device 1 rundel@tbBook [gp_pm25]$ open results/ rundel@tbBook [gp_pm25]$ rundel@tbBook [gp_pm25]$ docker images REPOSITORY TAG IMAGE ID CREATED SIZE rundel/ex_pm25_tidy latest 7579cad66121 22 minutes ago 1.91GB rundel/ex_pm25 latest e960520e38c3 26 minutes ago 1.89GB rocker/tidyverse 3.5.2 61266dee5826 9 hours ago 1.86GB rocker/tidyverse latest 61266dee5826 9 hours ago 1.86GB ubuntu 18.10 88fdd57278f5 8 days ago 73.7MB rundel@tbBook [gp_pm25]$ docker push rundel/ex_pm25 The push refers to repository [docker.io/rundel/ex_pm25] 2d7f3f5bc743: Pushed 2954675405c7: Mounted from rocker/tidyverse 56a7abe13e6c: Mounted from rocker/tidyverse 0125eb7aa0f4: Mounted from rocker/tidyverse 49f5b4becf12: Mounted from rocker/tidyverse bacef4718563: Mounted from rocker/tidyverse 0e626bcb4fa1: Mounted from rocker/tidyverse e8651103fd67: Mounted from rocker/tidyverse badfbcebf7f8: Mounted from rocker/tidyverse latest: digest: sha256:613207c140ff7ee183c9f4bbc8013e7a8ec8749608421de25408cffb4cc31e2f size: 2210 rundel@tbBook [gp_pm25]$ ssh cr173@rundel-rhel.colab.duke.edu cr173@rundel-rhel.colab.duke.edu's password: Last login: Thu Jan 31 11:43:49 2019 from 10.197.214.137 !! Important Notice about your RAPID VM !! This server is automatically set to patch and reboot every Sunday morning, between 3:00 AM and 4:00 AM. If you would like this behavior changed, you can do so by editing the file: /etc/cron.d/yum_autoupdate [cr173@vcm-8196 ~]$ [cr173@vcm-8196 ~]$ [cr173@vcm-8196 ~]$ cd [cr173@vcm-8196 ~]$ ls data example_pm25 R test.csv [cr173@vcm-8196 ~]$ cd example_pm25/ [cr173@vcm-8196 example_pm25]$ git pull remote: Enumerating objects: 9, done. remote: Counting objects: 100% (9/9), done. remote: Compressing objects: 100% (4/4), done. remote: Total 7 (delta 1), reused 7 (delta 1), pack-reused 0 Unpacking objects: 100% (7/7), done. From https://github.com/Sta790-Sp19/example_pm25 * [new branch] container -> origin/container Already up-to-date. [cr173@vcm-8196 example_pm25]$ ls analysis.R data gp_pm25.Rproj [cr173@vcm-8196 example_pm25]$ git checkout container Branch container set up to track remote branch container from origin. Switched to a new branch 'container' [cr173@vcm-8196 example_pm25]$ ls analysis.R command_args_demo.R data docker gp_pm25.Rproj [cr173@vcm-8196 example_pm25]$ git status # On branch container nothing to commit, working directory clean [cr173@vcm-8196 example_pm25]$ singularity pull docker://rundel/ex_pm25 WARNING: pull for Docker Hub is not guaranteed to produce the WARNING: same image on repeated pull. Use Singularity Registry WARNING: (shub://) to pull exactly equivalent images. Docker image path: index.docker.io/rundel/ex_pm25:latest Cache folder set to /home/cr173/.singularity/docker [8/8] |===================================| 100.0% Importing: base Singularity environment Exploding layer: sha256:ab1fc7e4bf9195e554669fafa47f69befe22053d7100f5f7002cb9254a36f37c.tar.gz Exploding layer: sha256:e4623974965c462a292c3273fdc808d4698ce3e065629e2df395b0b71c5c8d02.tar.gz Exploding layer: sha256:a6378d10729f74ab48d5eac929c035d8f9e5bfd793a23a5728f7caafdfe21344.tar.gz Exploding layer: sha256:774a8c9e81a267e101916a5e56b8c27cd98d92cef9ddbad95150f2bc06d082be.tar.gz Exploding layer: sha256:1782217cd0e7eb85883c013dcaaffc795ea209b042b0853fac69f184fd111a30.tar.gz Exploding layer: sha256:60ac9c54273c83cb0d248dddb83158fd843d4011ef8853b0edeed7584d25ea8b.tar.gz Exploding layer: sha256:674a4a01153ebdf0aeb4ea7df8da948e827a856faf2d90f4dda97aefc0bba95e.tar.gz Exploding layer: sha256:a77d4e8e6986e0594bc73a38e9f16371cc764a397aaef84b2612f3cc4939d9b8.tar.gz Exploding layer: sha256:b59592338dd06e458e72f79ea5df6eeb02116912801cc7f685e81dfb8b6d78ac.tar.gz Exploding layer: sha256:104914590c536854352f5016e003fabaf1a04ad803f71aafa95dd16c0472077a.tar.gz WARNING: Building container as an unprivileged user. If you run this container as root WARNING: it may be missing some functionality. Building Singularity image... Singularity container built: ./ex_pm25.simg Cleaning up... Done. Container is at: ./ex_pm25.simg [cr173@vcm-8196 example_pm25]$ ls analysis.R command_args_demo.R data docker ex_pm25.simg gp_pm25.Rproj [cr173@vcm-8196 example_pm25]$ singularity run --bind $(pwd):/work ex_pm25.simg analysis.R 1 Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) ---------------------------------------- General model description ---------------------------------------- Model fit with 110 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- Batch: 100 of 1000, 10.00% parameter acceptance tuning sigma.sq 58.0 0.85960 tau.sq 50.0 0.34257 phi 88.0 0.85960 ------------------------------------------------- Batch: 200 of 1000, 20.00% parameter acceptance tuning sigma.sq 46.0 1.53527 tau.sq 52.0 0.34949 phi 72.0 2.33662 ------------------------------------------------- Batch: 300 of 1000, 30.00% parameter acceptance tuning sigma.sq 38.0 1.50487 tau.sq 34.0 0.34949 phi 48.0 4.00966 ------------------------------------------------- Batch: 400 of 1000, 40.00% parameter acceptance tuning sigma.sq 42.0 1.53527 tau.sq 42.0 0.35655 phi 62.0 4.09066 ------------------------------------------------- Batch: 500 of 1000, 50.00% parameter acceptance tuning sigma.sq 36.0 1.41723 tau.sq 52.0 0.37859 phi 52.0 4.00966 ------------------------------------------------- Batch: 600 of 1000, 60.00% parameter acceptance tuning sigma.sq 46.0 1.66314 tau.sq 42.0 0.34257 phi 40.0 4.00966 ------------------------------------------------- Batch: 700 of 1000, 70.00% parameter acceptance tuning sigma.sq 46.0 1.56629 tau.sq 44.0 0.34257 phi 54.0 4.34362 ------------------------------------------------- Batch: 800 of 1000, 80.00% parameter acceptance tuning sigma.sq 32.0 1.47507 tau.sq 42.0 0.36375 phi 42.0 3.93027 ------------------------------------------------- Batch: 900 of 1000, 90.00% parameter acceptance tuning sigma.sq 42.0 1.50487 tau.sq 38.0 0.37110 phi 48.0 4.00966 ------------------------------------------------- Batch: 1000 of 1000, 100.00% parameter acceptance tuning sigma.sq 44.0 1.56629 tau.sq 52.0 0.34949 phi 50.0 4.43136 ------------------------------------------------- ---------------------------------------- General model description ---------------------------------------- Model fit with 110 observations. Prediction at 365 locations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. ------------------------------------------------- Sampling ------------------------------------------------- Sampled: 100 of 2500, 3.96% Sampled: 200 of 2500, 7.96% Sampled: 300 of 2500, 11.96% Sampled: 400 of 2500, 15.96% Sampled: 500 of 2500, 19.96% Sampled: 600 of 2500, 23.96% Sampled: 700 of 2500, 27.96% Sampled: 800 of 2500, 31.96% Sampled: 900 of 2500, 35.96% Sampled: 1000 of 2500, 39.96% Sampled: 1100 of 2500, 43.96% Sampled: 1200 of 2500, 47.96% Sampled: 1300 of 2500, 51.96% Sampled: 1400 of 2500, 55.96% Sampled: 1500 of 2500, 59.96% Sampled: 1600 of 2500, 63.96% Sampled: 1700 of 2500, 67.96% Sampled: 1800 of 2500, 71.96% Sampled: 1900 of 2500, 75.96% Sampled: 2000 of 2500, 79.96% Sampled: 2100 of 2500, 83.96% Sampled: 2200 of 2500, 87.96% Sampled: 2300 of 2500, 91.96% Sampled: 2400 of 2500, 95.96% Sampled: 2500 of 2500, 99.96% null device 1 [cr173@vcm-8196 example_pm25]$ ls analysis.R command_args_demo.R data docker ex_pm25.simg gp_pm25.Rproj results [cr173@vcm-8196 example_pm25]$ ls results/ 010030010 [cr173@vcm-8196 example_pm25]$ ls results/010030010/ data.rds pred.pdf pred.rds splm.rds [cr173@vcm-8196 example_pm25]$ cd .. [cr173@vcm-8196 ~]$ scp -R example_pm25/ cr173@smith.stat.duke.edu:~/ unknown option -- R usage: scp [-12346BCpqrv] [-c cipher] [-F ssh_config] [-i identity_file] [-l limit] [-o ssh_option] [-P port] [-S program] [[user@]host1:]file1 ... [[user@]host2:]file2 [cr173@vcm-8196 ~]$ scp -r example_pm25/ cr173@smith.stat.duke.edu:~/ The authenticity of host 'smith.stat.duke.edu (152.3.22.4)' can't be established. ECDSA key fingerprint is SHA256:eOkwBtEEnJuDWVlIQcomLGo9Wil+AioetV4i4B1Fi38. ECDSA key fingerprint is MD5:93:2f:50:63:4b:a5:9b:42:fe:1d:46:ae:a4:83:57:9d. Are you sure you want to continue connecting (yes/no)? yes Warning: Permanently added 'smith.stat.duke.edu,152.3.22.4' (ECDSA) to the list of known hosts. cr173@smith.stat.duke.edu's password: master 100% 41 6.6KB/s 00:00 container 100% 41 10.9KB/s 00:00 HEAD 100% 32 4.7KB/s 00:00 container 100% 41 5.8KB/s 00:00 description 100% 73 5.6KB/s 00:00 applypatch-msg.sample 100% 452 121.2KB/s 00:00 commit-msg.sample 100% 896 211.0KB/s 00:00 post-update.sample 100% 189 7.5KB/s 00:00 pre-applypatch.sample 100% 398 46.2KB/s 00:00 pre-commit.sample 100% 1704 253.4KB/s 00:00 pre-push.sample 100% 1348 107.5KB/s 00:00 pre-rebase.sample 100% 4951 866.5KB/s 00:00 prepare-commit-msg.sample 100% 1239 41.4KB/s 00:00 update.sample 100% 3611 827.2KB/s 00:00 exclude 100% 240 6.3KB/s 00:00 HEAD 100% 26 5.6KB/s 00:00 config 100% 340 97.0KB/s 00:00 eae6de5f30ca9e43b1fba3d7ecd373081b4f8b 100% 154 44.6KB/s 00:00 80f93632e292f4b01e1330434f38533ace0995 100% 127 11.1KB/s 00:00 d09611d7d420076603caa30af2a9c4b924e6d8 100% 158 24.8KB/s 00:00 2d9e47e0ceb9a10f7b8ea8d2cfd5d63eccfd85 100% 159 12.7KB/s 00:00 9ea203b34c95eb653fcf33c511a97ddfd87b2a 100% 57 13.0KB/s 00:00 d5dc7e627470c3910a90844fbb2f66668aac9e 100% 887 19.7KB/s 00:00 a409f094e8d5cf11a3224274fd1ed4c6a16638 100% 855 123.0KB/s 00:00 2ded2854431124f745e4d53017bbb9afd5d3fd 100% 52 13.1KB/s 00:00 22cef147985c9e770fdfc6af58ed88b5b4529d 100% 939KB 20.1MB/s 00:00 3c2ebc99e2e337f7d69948b93529a437590b27 100% 160 19.2KB/s 00:00 e4ec1577b69eb3de24c365c3101dd16fa1800d 100% 162 23.2KB/s 00:00 a55af50df04e5517ca2ac6e31eaae4c7a1e595 100% 230 43.1KB/s 00:00 9134d31d10e085bd7d0fc04791064db4e61feb 100% 975 188.6KB/s 00:00 9f868051a1e2ab400340e781cbc9ca39d19772 100% 65 12.4KB/s 00:00 caa1b18ceb18e4d7924628f066d1d3fc22f8c1 100% 89 15.4KB/s 00:00 817871a6d46fdeb73265c0a46d27b71497117a 100% 156 14.0KB/s 00:00 426188770f6d6f3df3624a5ddfbaaf9697a7e1 100% 62 11.0KB/s 00:00 packed-refs 100% 107 10.6KB/s 00:00 HEAD 100% 201 44.7KB/s 00:00 container 100% 153 15.9KB/s 00:00 master 100% 201 34.7KB/s 00:00 container 100% 192 37.0KB/s 00:00 HEAD 100% 384 52.8KB/s 00:00 index 100% 616 136.5KB/s 00:00 FETCH_HEAD 100% 226 55.7KB/s 00:00 ORIG_HEAD 100% 41 6.5KB/s 00:00 .gitignore 100% 48 15.5KB/s 00:00 frm.csv 100% 6618KB 24.9MB/s 00:00 gp_pm25.Rproj 100% 205 16.4KB/s 00:00 analysis.R 100% 2082 187.4KB/s 00:00 command_args_demo.R 100% 49 1.5KB/s 00:00 Dockerfile 100% 173 36.0KB/s 00:00 Dockerfile_tidybayes 100% 46 1.2KB/s 00:00 ex_pm25.simg 100% 657MB 43.8MB/s 00:15 data.rds 100% 676 44.4KB/s 00:00 splm.rds 100% 522KB 1.4MB/s 00:00 pred.rds 100% 8308 459.8KB/s 00:00 pred.pdf 100% 8632 1.3MB/s 00:00 [cr173@vcm-8196 ~]$ ssh cr173@smith.stat.duke.edu cr173@smith.stat.duke.edu's password: Last login: Mon Jan 28 21:47:29 2019 from 162.202.220.77 cr173@smith [~]$ cd example_pm25/ cr173@smith [example_pm25]$ ls analysis.R command_args_demo.R data docker ex_pm25.simg gp_pm25.Rproj results cr173@smith [example_pm25]$ cr173@smith [example_pm25]$ ls analysis.R command_args_demo.R data docker ex_pm25.simg gp_pm25.Rproj results cr173@smith [example_pm25]$ singularity run --bind $(pwd):/work ex_pm25.simg analysis.R 2& > 2.out [1] 26977 cr173@smith [example_pm25]$ singularity run --bind $(pwd):/work ex_pm25.simg analysis.R 2& > 2.out Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) ---------------------------------------- General model description ---------------------------------------- Model fit with 120 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- [2] 27058 cr173@smith [example_pm25]$ singularity run --bind $(pwd):/work ex_pm25.simg analysis.R 2& > 2.out Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda Loading required package: magic Loading required package: abind Loading required package: Formula Parsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) ---------------------------------------- General model description ---------------------------------------- Model fit with 120 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- cr173@smith [example_pm25]$ singularity run --bind $(pwd):/work ex_pm25.simg analysis.R 3& > 3.out [3] 27135 cr173@smith [example_pm25]$ Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union Loading required package: coda sLoading required package: magic Loading required package: abind Loading required package: Formula udo hParsed with column specification: cols( site = col_character(), date = col_datetime(format = ""), latitude = col_double(), longitude = col_double(), pm25 = col_double() ) tip---------------------------------------- General model description ---------------------------------------- Model fit with 116 observations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. Using adaptive MCMC. Number of batches 1000. Batch length 50. Target acceptance rate 0.43000. Priors and hyperpriors: beta normal: mu: 0.000 cov: 1000.000 sigma.sq IG hyperpriors shape=2.00000 and scale=2.00000 tau.sq IG hyperpriors shape=2.00000 and scale=0.10000 phi Unif hyperpriors a=0.05773 and b=0.05774 ------------------------------------------------- Sampling ------------------------------------------------- cr173@smith [example_pm25]$ sudo htop [sudo] password for cr173: cr173@smith [example_pm25]$ cr173@smith [example_pm25]$ ls 2.out 3.out analysis.R command_args_demo.R data docker ex_pm25.simg gp_pm25.Rproj results cr173@smith [example_pm25]$ cd results/ cr173@smith [results]$ ls 010030010 cr173@smith [results]$ Batch: 200 of 1000, 20.00% parameter acceptance tuning sigma.sq 36.0 1.11484 tau.sq 56.0 0.34949 phi 60.0 2.33662 ------------------------------------------------- Batch: 200 of 1000, 20.00% parameter acceptance tuning sigma.sq 42.0 1.20769 tau.sq 42.0 0.35655 phi 68.0 2.33662 ------------------------------------------------- Batch: 200 of 1000, 20.00% parameter acceptance tuning sigma.sq 40.0 1.09276 tau.sq 54.0 0.34949 phi 68.0 2.33662 ------------------------------------------------- cr173@smith [results]$ Batch: 300 of 1000, 30.00% parameter acceptance tuning sigma.sq 58.0 1.16033 tau.sq 36.0 0.34949 phi 36.0 3.85244 ------------------------------------------------- Batch: 300 of 1000, 30.00% parameter acceptance tuning sigma.sq 42.0 1.23208 tau.sq 50.0 0.34257 phi 54.0 4.25761 ------------------------------------------------- Batch: 400 of 1000, 40.00% parameter acceptance tuning sigma.sq 44.0 1.11484 tau.sq 44.0 0.34949 phi 40.0 4.25761 ------------------------------------------------- Batch: 300 of 1000, 30.00% parameter acceptance tuning sigma.sq 44.0 1.20769 tau.sq 40.0 0.35655 phi 56.0 3.85244 ------------------------------------------------- Batch: 400 of 1000, 40.00% parameter acceptance tuning sigma.sq 54.0 1.28237 tau.sq 42.0 0.34257 phi 50.0 4.00966 ------------------------------------------------- Batch: 500 of 1000, 50.00% parameter acceptance tuning sigma.sq 44.0 1.20769 tau.sq 30.0 0.35655 phi 32.0 4.34362 ------------------------------------------------- cr173@smith [results]$ Batch: 600 of 1000, 60.00% parameter acceptance tuning sigma.sq 52.0 1.16033 tau.sq 44.0 0.35655 phi 38.0 4.09066 ------------------------------------------------- Batch: 500 of 1000, 50.00% parameter acceptance tuning sigma.sq 58.0 1.18377 tau.sq 50.0 0.34257 phi 52.0 4.17330 ------------------------------------------------- Batch: 400 of 1000, 40.00% parameter acceptance tuning sigma.sq 40.0 1.13736 tau.sq 46.0 0.34257 phi 40.0 4.43136 ------------------------------------------------- Batch: 700 of 1000, 70.00% parameter acceptance tuning sigma.sq 58.0 1.13736 tau.sq 46.0 0.33578 phi 36.0 4.17330 ------------------------------------------------- cr173@smith [results]$ Batch: 600 of 1000, 60.00% parameter acceptance tuning sigma.sq 46.0 1.16033 tau.sq 44.0 0.37859 phi 38.0 3.93027 ------------------------------------------------- Batch: 500 of 1000, 50.00% parameter acceptance tuning sigma.sq 38.0 1.13736 tau.sq 40.0 0.36375 phi 38.0 4.34362 ------------------------------------------------- Batch: 800 of 1000, 80.00% parameter acceptance tuning sigma.sq 44.0 1.18377 tau.sq 40.0 0.34949 phi 38.0 4.25761 ------------------------------------------------- Batch: 600 of 1000, 60.00% parameter acceptance tuning sigma.sq 46.0 1.18377 tau.sq 46.0 0.34949 phi 30.0 4.17330 ------------------------------------------------- Batch: 700 of 1000, 70.00% parameter acceptance tuning sigma.sq 32.0 1.18377 tau.sq 56.0 0.34949 phi 40.0 4.00966 ------------------------------------------------- Batch: 900 of 1000, 90.00% parameter acceptance tuning sigma.sq 42.0 1.02912 tau.sq 34.0 0.34257 phi 44.0 4.00966 ------------------------------------------------- Batch: 700 of 1000, 70.00% parameter acceptance tuning sigma.sq 46.0 1.11484 tau.sq 58.0 0.34949 phi 36.0 4.25761 ------------------------------------------------- Batch: 1000 of 1000, 100.00% parameter acceptance tuning sigma.sq 42.0 1.16033 tau.sq 42.0 0.34949 phi 46.0 4.25761 ------------------------------------------------- ---------------------------------------- General model description ---------------------------------------- Model fit with 120 observations. Prediction at 365 locations. Number of covariates 1 (including intercept if specified). Using the gaussian spatial correlation model. ------------------------------------------------- Sampling ------------------------------------------------- Sampled: 100 of 2500, 3.96% Sampled: 200 of 2500, 7.96% Sampled: 300 of 2500, 11.96% Sampled: 400 of 2500, 15.96% Sampled: 500 of 2500, 19.96% Sampled: 600 of 2500, 23.96% Sampled: 700 of 2500, 27.96% Batch: 800 of 1000, 80.00% parameter acceptance tuning sigma.sq 46.0 1.16033 tau.sq 54.0 0.35655 phi 46.0 4.17330 ------------------------------------------------- Sampled: 800 of 2500, 31.96% Sampled: 900 of 2500, 35.96% Sampled: 1000 of 2500, 39.96% Sampled: 1100 of 2500, 43.96% Sampled: 1200 of 2500, 47.96% Sampled: 1300 of 2500, 51.96% Sampled: 1400 of 2500, 55.96% Sampled: 1500 of 2500, 59.96% Sampled: 1600 of 2500, 63.96% Sampled: 1700 of 2500, 67.96% Sampled: 1800 of 2500, 71.96% Sampled: 1900 of 2500, 75.96% Sampled: 2000 of 2500, 79.96% Sampled: 2100 of 2500, 83.96% Sampled: 2200 of 2500, 87.96% Sampled: 2300 of 2500, 91.96% Sampled: 2400 of 2500, 95.96% Sampled: 2500 of 2500, 99.96% null device 1 Batch: 800 of 1000, 80.00% parameter acceptance tuning sigma.sq 38.0 1.13736 tau.sq 44.0 0.34949 phi 42.0 4.25761 ------------------------------------------------- Batch: 900 of 1000, 90.00% parameter acceptance tuning sigma.sq 34.0 1.23208 tau.sq 38.0 0.35655 phi 40.0 4.09066 -------------------------------------------------