Greeting all,
I am attempting to install OpenMx on a x86_64 Redhat Linux cluster running R 3.3.1. I am installing it using the command source('https://openmx.ssri.psu.edu/getOpenMx.R').
Based on the errors I am getting it looks as if R is not invoking a compiler. Here is the full output of what I am getting:
> source('https://openmx.ssri.psu.edu/getOpenMx.R') You are now installing the latest version of OpenMx.--- Please select a CRAN mirror for use in this session --- HTTPS CRAN mirror 1: 0-Cloud [https] 2: Algeria [https] 3: Australia (Canberra) [https] 4: Australia (Melbourne) [https] 5: Australia (Perth) [https] 6: Austria [https] 7: Belgium (Ghent) [https] 8: Brazil (RJ) [https] 9: Brazil (SP 1) [https] 10: Bulgaria [https] 11: Canada (MB) [https] 12: Chile 1 [https] 13: Chile 2 [https] 14: China (Beijing) [https] 15: China (Hefei) [https] 16: China (Lanzhou) [https] 17: Colombia (Cali) [https] 18: Czech Republic [https] 19: Denmark [https] 20: Estonia [https] 21: France (Lyon 1) [https] 22: France (Lyon 2) [https] 23: France (Marseille) [https] 24: France (Montpellier) [https] 25: France (Paris 2) [https] 26: Germany (Göttingen) [https] 27: Germany (Münster) [https] 28: Iceland [https] 29: India [https] 30: Indonesia (Jakarta) [https] 31: Ireland [https] 32: Italy (Padua) [https] 33: Japan (Tokyo) [https] 34: Malaysia [https] 35: Mexico (Mexico City) [https] 36: New Zealand [https] 37: Norway [https] 38: Philippines [https] 39: Russia (Moscow) [https] 40: Serbia [https] 41: Spain (A Coruña) [https] 42: Spain (Madrid) [https] 43: Sweden [https] 44: Switzerland [https] 45: Taiwan (Chungli) [https] 46: Turkey (Denizli) [https] 47: Turkey (Mersin) [https] 48: UK (Bristol) [https] 49: UK (Cambridge) [https] 50: UK (London 1) [https] 51: USA (CA 1) [https] 52: USA (IA) [https] 53: USA (IN) [https] 54: USA (KS) [https] 55: USA (MI 1) [https] 56: USA (OR) [https] 57: USA (TN) [https] 58: USA (TX 1) [https] 59: USA (TX 2) [https] 60: (HTTP mirrors) Selection: 51 also installing the dependency ‘xml2’ trying URL 'https://cran.cnr.berkeley.edu/src/contrib/xml2_1.1.1.tar.gz' Content type 'application/x-gzip' length 244643 bytes (238 KB) ================================================== downloaded 238 KB trying URL 'https://cran.cnr.berkeley.edu/src/contrib/roxygen2_6.0.1.tar.gz' Content type 'application/x-gzip' length 150580 bytes (147 KB) ================================================== downloaded 147 KB * installing *source* package ‘xml2’ ... ** package ‘xml2’ successfully unpacked and MD5 sums checked Found pkg-config cflags and libs! Using PKG_CFLAGS=-I/usr/include/libxml2 Using PKG_LIBS=-lxml2 -lz -lm ** libs g++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o g++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -fpic -g -O2 -c connection.cpp -o connection.o g++ -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I../inst/include -I/usr/include/libxml2 -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -fpic -g -O2 -c xml2_doc.cpp -o xml2_doc.o xml2_doc.cpp: In function ‘Rcpp::IntegerVector xml_parse_options()’: xml2_doc.cpp:82:5: error: ‘XML_PARSE_OLD10’ was not declared in this scope xml2_doc.cpp:83:5: error: ‘XML_PARSE_NOBASEFIX’ was not declared in this scope xml2_doc.cpp:84:5: error: ‘XML_PARSE_HUGE’ was not declared in this scope xml2_doc.cpp:85:5: error: ‘XML_PARSE_OLDSAX’ was not declared in this scope make: *** [xml2_doc.o] Error 1 ERROR: compilation failed for package ‘xml2’ * removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/xml2’ ERROR: dependency ‘xml2’ is not available for package ‘roxygen2’ * removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/roxygen2’ The downloaded source packages are in ‘/tmp/Rtmp7H0wdr/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done trying URL 'https://openmx.ssri.psu.edu/OpenMx2/src/contrib/OpenMx_2.7.10.tar.gz' Content type 'application/x-gzip' length 4739360 bytes (4.5 MB) ================================================== downloaded 4.5 MB * installing *source* package ‘OpenMx’ ... NOTE: ./configure is not an autoconf generated script. Change default C/C++ compiler and default compile flags by editing ~/.R/Makevars ** libs I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c Compute.cpp -o Compute.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [Compute.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c ComputeGD.cpp -o ComputeGD.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [ComputeGD.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c ComputeNM.cpp -o ComputeNM.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [ComputeNM.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c ComputeNR.cpp -o ComputeNR.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [ComputeNR.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c ComputeSD.cpp -o ComputeSD.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [ComputeSD.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c FellnerFitFunction.cpp -o FellnerFitFunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [FellnerFitFunction.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c MarkovExpectation.cpp -o MarkovExpectation.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [MarkovExpectation.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c MarkovFF.cpp -o MarkovFF.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [MarkovFF.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c ba81quad.cpp -o ba81quad.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [ba81quad.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c dmvnorm.cpp -o dmvnorm.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [dmvnorm.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c fitMultigroup.cpp -o fitMultigroup.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [fitMultigroup.o] Error 127 (ignored) gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fpic -g -O2 -c general.c -o general.o I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c glue.cpp -o glue.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [glue.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c matrix.cpp -o matrix.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [matrix.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c merge.cpp -o merge.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [merge.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c nanotimer.cpp -o nanotimer.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [nanotimer.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c nloptcpp.cpp -o nloptcpp.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [nloptcpp.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxAlgebra.cpp -o omxAlgebra.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxAlgebra.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxAlgebraFitFunction.cpp -o omxAlgebraFitFunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxAlgebraFitFunction.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxData.cpp -o omxData.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxData.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxExpectation.cpp -o omxExpectation.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxExpectation.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxExpectationBA81.cpp -o omxExpectationBA81.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxExpectationBA81.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxExportBackendState.cpp -o omxExportBackendState.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxExportBackendState.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxFIMLFitFunction.cpp -o omxFIMLFitFunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxFIMLFitFunction.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxFIMLSingleIteration.cpp -o omxFIMLSingleIteration.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxFIMLSingleIteration.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxFitFunction.cpp -o omxFitFunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxFitFunction.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxFitFunctionBA81.cpp -o omxFitFunctionBA81.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxFitFunctionBA81.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxGREMLExpectation.cpp -o omxGREMLExpectation.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxGREMLExpectation.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxGREMLfitfunction.cpp -o omxGREMLfitfunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxGREMLfitfunction.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxHessianCalculation.cpp -o omxHessianCalculation.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxHessianCalculation.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxImportFrontendState.cpp -o omxImportFrontendState.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxImportFrontendState.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxLISRELExpectation.cpp -o omxLISRELExpectation.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxLISRELExpectation.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxMLFitFunction.cpp -o omxMLFitFunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxMLFitFunction.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxMatrix.cpp -o omxMatrix.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxMatrix.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxNPSOLSpecific.cpp -o omxNPSOLSpecific.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxNPSOLSpecific.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxNormalExpectation.cpp -o omxNormalExpectation.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxNormalExpectation.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxRAMExpectation.cpp -o omxRAMExpectation.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxRAMExpectation.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxRFitFunction.cpp -o omxRFitFunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxRFitFunction.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxRowFitFunction.cpp -o omxRowFitFunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxRowFitFunction.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxState.cpp -o omxState.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxState.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxStateSpaceExpectation.cpp -o omxStateSpaceExpectation.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxStateSpaceExpectation.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxSymbolTable.cpp -o omxSymbolTable.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxSymbolTable.o] Error 127 (ignored) I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c omxWLSFitFunction.cpp -o omxWLSFitFunction.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [omxWLSFitFunction.o] Error 127 (ignored) gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fpic -g -O2 -c optimize.c -o optimize.o gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fpic -g -O2 -c options.c -o options.o gfortran -fpic -g -O2 -c sadmvn.f -o sadmvn.o gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fpic -g -O2 -c slsqp.c -o slsqp.o I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c ssMLFit.cpp -o ssMLFit.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [ssMLFit.o] Error 127 (ignored) gcc -std=gnu99 -I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fpic -g -O2 -c stop.c -o stop.o I/exports/apps/R/R-3.3.1/lib64/R/include -DNDEBUG -I/exports/apps/libs/include -I"/exports/apps/R/R-3.3.1/lib64/R/library/Rcpp/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/RcppEigen/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/StanHeaders/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/BH/include" -I"/exports/apps/R/R-3.3.1/lib64/R/library/rpf/include" -fopenmp -Wall -Wno-unknown-pragmas -Wno-unused-parameter -Wvla -Wno-unused-local-typedefs -Wno-deprecated-declarations -Wno-unused-function -c subnp.cpp -o subnp.o /bin/sh: I/exports/apps/R/R-3.3.1/lib64/R/include: No such file or directory make: [subnp.o] Error 127 (ignored) -shared -L/exports/apps/libs/lib -o OpenMx.so Compute.o ComputeGD.o ComputeNM.o ComputeNR.o ComputeSD.o FellnerFitFunction.o MarkovExpectation.o MarkovFF.o ba81quad.o dmvnorm.o fitMultigroup.o general.o glue.o matrix.o merge.o nanotimer.o nloptcpp.o omxAlgebra.o omxAlgebraFitFunction.o omxData.o omxExpectation.o omxExpectationBA81.o omxExportBackendState.o omxFIMLFitFunction.o omxFIMLSingleIteration.o omxFitFunction.o omxFitFunctionBA81.o omxGREMLExpectation.o omxGREMLfitfunction.o omxHessianCalculation.o omxImportFrontendState.o omxLISRELExpectation.o omxMLFitFunction.o omxMatrix.o omxNPSOLSpecific.o omxNormalExpectation.o omxRAMExpectation.o omxRFitFunction.o omxRowFitFunction.o omxState.o omxStateSpaceExpectation.o omxSymbolTable.o omxWLSFitFunction.o optimize.o options.o sadmvn.o slsqp.o ssMLFit.o stop.o subnp.o -fopenmp -lgfortran -lm -L/exports/apps/R/R-3.3.1/lib64/R/lib -lRblas -L/exports/apps/R/R-3.3.1/lib64/R/lib -lRlapack -L../src -lnpsol -lgfortran -lm /bin/sh: line 2: -shared: command not found make: *** [OpenMx.so] Error 127 ERROR: compilation failed for package ‘OpenMx’ * removing ‘/exports/apps/R/R-3.3.1/lib64/R/library/OpenMx’ The downloaded source packages are in ‘/tmp/Rtmp7H0wdr/downloaded_packages’ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning messages: 1: In install.packages(pkg) : installation of package ‘xml2’ had non-zero exit status 2: In install.packages(pkg) : installation of package ‘roxygen2’ had non-zero exit status 3: In install.packages(pkgs = c("OpenMx"), contriburl = contrib.url(repos, : installation of package ‘OpenMx’ had non-zero exit status
I tried adding a .R/Makevars file in order to force it to use a compiler, but got the roughly the same output. The only difference is that when it did invoke a compiler it invoked the compiler I specified in the Makevars file (mpicc or mpic++) instead of the generic gnu compiler. Here is a copy of my Makevars file:
C=mpicc CFLAGS=-O3 -ffast-math -fopenmp CXX=mpic++ FC=mpif90 FCFLAGS=-O3 -ffast-math -fopenmp
Thanks in advance for any help you can give me!
Shane
P.s. I am running OpenMpi 1.4.2