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
Try setting CXX1X in addition to CXX. I'm not sure if mpic++ can build the OpenMx source code, but it's worth a try.
So I think that helped. However, I got a new error.
Also you mentioned that mpic++ won't compile the OpenMx source code. However, if I want to run it with OpenMPI then what do I compile it with?
Thanks,
Shane
Like many R extensions, OpenMx requires C++11. What is mpic++ ? Is it based on gcc? Which version?
mpic++ is just a wrapper for g++ which allows for parallel computing. I am using gcc version 4.7 as my back end compiler. According to https://gcc.gnu.org/gcc-4.7/cxx0x_status.html it looks like gcc/4.7 may not have full c++11 support. I will look into upgrading my version of gcc and get back to you. Thanks for your help so far!
Shane
Ah, OK. You need at least gcc version 4.9.
Thanks for all your help so far. I installed gcc/4.9.3 updated my Makevars file and despite one small error (shown in log below) got OpenMx to compile. However, I tried running a simple model
and got the following error
I tried that same model on my laptop (which is more up to date, but only has 4 cores) and it works perfectly, so I am assuming that it is still and issue with the compilation. Any ideas on what went wrong?
As always thanks for your continuing support. Much obliged,
Shane
P.S here is the output from the "successful" compilation
The message you're seeing is a warning, not an error; if it were an error, it would have been fatal to
mxRun()
, which would not have returned a value. The warning you're seeing concerns the quality of OpenMx's obtained solution, and is not even that uncommon. In this particular case, I strongly suspect the warning is spurious. Since the release of v2.7.11, we've changed OpenMx's criterion for an "acceptable" unconstrained solution to something more reasonable, so spurious warnings of this sort should be less common in future releases.So, I doubt it's a sign that something went wrong while compiling. I admit I'm a bit surprised that you ran the same model on a different system and got no warning. Were both systems running OpenMx v2.7.11, and on the same platform (try
mxVersion()
)? Also, are the solutions substantially equivalent (usesummary(factorModelFit)
)?Here are the outputs from both runs
laptop:
Server
Thanks,
Shane
Hmm, OK, there definitely seems to be something wrong here.
I was wondering if the choices that mpic++ is making re: compiler flags are somehow breaking the build. What do
return?
A higher version of the gnu compiler than 4.9 should also work (might even fix the problem) and could further improve performance.
Just as a sidebar, I feel like I am getting a slight hint that this module is not often compiled using mpi. Does this module not work well in parallel? Is it not used in parallel often? I am installing this program on a cluster on behalf of a researcher, so I am not very familiar with it myself. I know R can can be, and is used, for parallel computing tasks all the time, but I am unsure if OpenMx is. If this is the case I let the professor know that and we can compile it without mpi. Then he can do his normal R work in parallel and the OpenMx work can be done on a single core.
Thanks for all your help,
Shane
Can we have an update? Are things still broken? If all the estimates are coming out NA, perhaps you could turn on checkpointing. Use mxRun(..., checkpoint=TRUE). This will create a model.omx file in the current directory that might be helpful to diagnose what is going wrong.
So I was waiting for a response to my questions about whether or not Mx is often used in Parallel. I had questions since AdminNeale posted a response with the title "Parallel?" as well as AdminJosh asking the question "What is mpic++ ? Is it based on gcc?" These things made me wonder if it was not common practice to compile in parallel, or if it was even possible. I wanted to make sure I was not wasting my time attempting to compile with OpenMpi. Additionally, I never got a response about whether or not my outputs to
mpic++ -showme, mpicc -showme:compile and mpicc -showme:link
were acceptable or if there was something wrong with them. Finally here is an output from the sample simulation using checkpoint=TRUEI am truly at a loss as to what to try next. Any suggestions would be great, and please let me know if I should continue attempting to compile in parallel or if that is just a waste of time.
Thanks,
Shane
Can you attach the checkpoint output? It should be in a file named "One Factor.omx" in the current directory.
Yes, OpenMx does have support for multithreading, with OpenMP. However, the package is only routinely tested with gcc and clang, not with the Mpi toolset. It might be worth trying to compile it without parallel, to see if that makes a difference.
Concerning checkpointing, was there a file written in R's working directory when the MxModel was run? That's where checkpointing output goes. It's possible there was no file written, since I don't know how well checkpointing works with the default mxOptions. You could try
Sorry about that I missed the extra file in the directory. I thought the checkpointing put additional output to the terminal. My bad.
Shane
p.s. I renamed the file to One Factor.txt since the site would not let me upload a file with extension omx
Ah, well, it looks like things are going wrong really early. Like Rob said, we don't do a lot of testing with MPI. If you need to make OpenMx work with MPI then you're going to need some software developers to figure out what is going wrong.
Sorry I haven't posted in a while, but I tried recompiling without using OpenMpi and that did fix the problems. So I'll just have to figure out what MPI is doing that is breaking things.