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OpenMx Installation on Redhat Cluster

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Joined: 04/13/2017 - 11:44
OpenMx Installation on Redhat Cluster

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('http://openmx.psyc.virginia.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('http://openmx.psyc.virginia.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 'http://openmx.psyc.virginia.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

AdminJosh's picture
Offline
Joined: 12/12/2012 - 12:15
CXX1X CXX11

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.

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
CXX1X

So I think that helped. However, I got a new error.

> source('http://openmx.psyc.virginia.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
mpic++ -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
mpic++ -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
mpic++ -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/RtmpQyUo00/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
trying URL 'http://openmx.psyc.virginia.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
mpic++  -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
Compute.cpp: In member function ‘std::string FitContext::getIterationError():
Compute.cpp:898:4: warning: ‘auto’ changes meaning in C++11; please remove it [-Wc++0x-compat]
Compute.cpp:898:10: error: ISO C++ forbids declaration of ‘strwith no type [-fpermissive]
Compute.cpp:898:31: error: invalid initialization of reference of type ‘int&’ from expression of type ‘std::string {aka std::basic_string<char>}’
Compute.cpp:899:13: error: request for member ‘size’ instr’, which is of non-class type ‘int’
Compute.cpp:900:55: error: request for member ‘c_str’ instr’, which is of non-class type ‘int’
make: *** [Compute.o] Error 1
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/RtmpQyUo00/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

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

AdminJosh's picture
Offline
Joined: 12/12/2012 - 12:15
mpic++

Like many R extensions, OpenMx requires C++11. What is mpic++ ? Is it based on gcc? Which version?

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
mpic++

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

AdminJosh's picture
Offline
Joined: 12/12/2012 - 12:15
gcc version

Ah, OK. You need at least gcc version 4.9.

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
OpenMx Compiled but won't run properly

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

require(OpenMx)
data(demoOneFactor)
factorModel <- mxModel("One Factor",
      mxMatrix("Full", 5, 1, values=0.8,
           free=TRUE, name="A"),
      mxMatrix("Symm", 1, 1, values=1,
           free=FALSE, name="L"),
      mxMatrix("Diag", 5, 5, values=1,
           free=TRUE, name="U"),
      mxAlgebra(A %*% L %*% t(A) + U, name="R"),
      mxExpectationNormal(covariance = "R",
            dimnames = names(demoOneFactor)),
      mxFitFunctionML(),
      mxData(cov(demoOneFactor), type="cov", numObs=500))
factorModelFit <- mxRun(factorModel)

and got the following error

Running One Factor with 10 parameters
Warning message:
In model 'One Factor' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED)

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

> source('http://openmx.psyc.virginia.edu/getOpenMx.R')
You are now installing the latest version of OpenMx.trying URL 'http://openmx.psyc.virginia.edu/OpenMx2/src/contrib/OpenMx_2.7.11.tar.gz'
Content type 'application/x-gzip' length 4754607 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
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c Compute.cpp -o Compute.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ComputeGD.cpp -o ComputeGD.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ComputeNM.cpp -o ComputeNM.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ComputeNR.cpp -o ComputeNR.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ComputeSD.cpp -o ComputeSD.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c FellnerFitFunction.cpp -o FellnerFitFunction.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c MarkovExpectation.cpp -o MarkovExpectation.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c MarkovFF.cpp -o MarkovFF.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ba81quad.cpp -o ba81quad.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c dmvnorm.cpp -o dmvnorm.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c fitMultigroup.cpp -o fitMultigroup.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  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c general.c -o general.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c glue.cpp -o glue.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c matrix.cpp -o matrix.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c merge.cpp -o merge.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c nanotimer.cpp -o nanotimer.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c nloptcpp.cpp -o nloptcpp.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxAlgebra.cpp -o omxAlgebra.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxAlgebraFitFunction.cpp -o omxAlgebraFitFunction.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxData.cpp -o omxData.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxExpectation.cpp -o omxExpectation.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxExpectationBA81.cpp -o omxExpectationBA81.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxExportBackendState.cpp -o omxExportBackendState.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxFIMLFitFunction.cpp -o omxFIMLFitFunction.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxFIMLSingleIteration.cpp -o omxFIMLSingleIteration.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxFitFunction.cpp -o omxFitFunction.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxFitFunctionBA81.cpp -o omxFitFunctionBA81.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxGREMLExpectation.cpp -o omxGREMLExpectation.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxGREMLfitfunction.cpp -o omxGREMLfitfunction.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxHessianCalculation.cpp -o omxHessianCalculation.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxImportFrontendState.cpp -o omxImportFrontendState.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxLISRELExpectation.cpp -o omxLISRELExpectation.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxMLFitFunction.cpp -o omxMLFitFunction.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxMatrix.cpp -o omxMatrix.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxNPSOLSpecific.cpp -o omxNPSOLSpecific.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxNormalExpectation.cpp -o omxNormalExpectation.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxRAMExpectation.cpp -o omxRAMExpectation.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxRFitFunction.cpp -o omxRFitFunction.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxRowFitFunction.cpp -o omxRowFitFunction.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxState.cpp -o omxState.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxStateSpaceExpectation.cpp -o omxStateSpaceExpectation.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxSymbolTable.cpp -o omxSymbolTable.o
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c omxWLSFitFunction.cpp -o omxWLSFitFunction.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  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c optimize.c -o optimize.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
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  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c options.c -o options.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
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  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c slsqp.c -o slsqp.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c ssMLFit.cpp -o ssMLFit.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  -O3 -ffast-math -fopenmp -std=c++11 -fpic -c stop.c -o stop.o
cc1: warning: command line option ‘-std=c++11is valid for C++/ObjC++ but not for C
mpic++  -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      -O3 -ffast-math -fopenmp -std=c++11 -fpic -c subnp.cpp -o subnp.o
mpic++ -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
mkdir -p ../inst/debug
cp *.gcno ../inst/debug/
cp: cannot stat `*.gcno': No such file or directory
make: [save-gcno] Error 1 (ignored)
installing to /exports/apps/R/R-3.3.1/lib64/R/library/OpenMx/libs
** R
** data
*** moving datasets to lazyload DB
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘print’ from package ‘base’ in package ‘OpenMx’
Creating a generic function for ‘nrow’ from package ‘base’ in package ‘OpenMx’
Creating a generic function for ‘ncol’ from package ‘base’ in package ‘OpenMx’
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (OpenMx)
 
The downloaded source packages are in
        ‘/tmp/RtmpqI1NIt/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
AdminRobK's picture
Offline
Joined: 01/24/2014 - 12:15
warning, not error; compilation probably OK
However, I tried running a simple model

require(OpenMx)
data(demoOneFactor)
factorModel <- mxModel("One Factor",
      mxMatrix("Full", 5, 1, values=0.8,
           free=TRUE, name="A"),
      mxMatrix("Symm", 1, 1, values=1,
           free=FALSE, name="L"),
      mxMatrix("Diag", 5, 5, values=1,
           free=TRUE, name="U"),
      mxAlgebra(A %*% L %*% t(A) + U, name="R"),
      mxExpectationNormal(covariance = "R",
            dimnames = names(demoOneFactor)),
      mxFitFunctionML(),
      mxData(cov(demoOneFactor), type="cov", numObs=500))
factorModelFit <- mxRun(factorModel)

and got the following error

Running One Factor with 10 parameters
Warning message:
In model 'One Factor' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED)

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?

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 (use summary(factorModelFit))?

Shesprich's picture
Offline
Joined: 04/13/2017 - 11:44
Outputs

Here are the outputs from both runs

laptop:

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 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.
 
  Natural language support but running in an English locale
 
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.
 
> require(OpenMx)
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(NULL, 'Number of Threads', parallel::detectCores())
> data(demoOneFactor)
> factorModel <- mxModel("One Factor",
+       mxMatrix("Full", 5, 1, values=0.8,
+            free=TRUE, name="A"),
+       mxMatrix("Symm", 1, 1, values=1,
+            free=FALSE, name="L"),
+       mxMatrix("Diag", 5, 5, values=1,
+            free=TRUE, name="U"),
+       mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+       mxExpectationNormal(covariance = "R",
+             dimnames = names(demoOneFactor)),
+       mxFitFunctionML(),
+       mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorModelFit <- mxRun(factorModel)
Running One Factor with 10 parameters
> summary(factorModelFit)
Summary of One Factor 
 
free parameters:
                name matrix row col   Estimate   Std.Error A
1  One Factor.A[1,1]      A   1   1 0.39675442 0.015518623  
2  One Factor.A[2,1]      A   2   1 0.50315690 0.018196001  
3  One Factor.A[3,1]      A   3   1 0.57666351 0.020407447  
4  One Factor.A[4,1]      A   4   1 0.70207009 0.023963327  
5  One Factor.A[5,1]      A   5   1 0.79545281 0.026616042  
6  One Factor.U[1,1]      U   1   1 0.04073255 0.002804281  
7  One Factor.U[2,2]      U   2   2 0.03794394 0.002797378  
8  One Factor.U[3,3]      U   3   3 0.04074551 0.003142855  
9  One Factor.U[4,4]      U   4   4 0.03930827 0.003398652  
10 One Factor.U[5,5]      U   5   5 0.03621453 0.003667530  
 
Model Statistics: 
               |  Parameters  |  Degrees of Freedom  |  Fit (-2lnL units)
       Model:             10                      5            -3660.5967
   Saturated:             15                      0            -3667.9905
Independence:              5                     10               64.5342
Number of observations/statistics: 500/15
 
chi-square:  χ² ( df=5 ) = 7.393793,  p = 0.1929616
Information Criteria: 
      |  df Penalty  |  Parameters Penalty  |  Sample-Size Adjusted
AIC:      -2.606207               27.39379                       NA
BIC:     -23.679247               69.53987                 37.79926
CFI: 0.9993569 
TLI: 0.9987139   (also known as NNFI) 
RMSEA:  0.03094378  [95% CI (0, 0.08143354)]
Prob(RMSEA <= 0.05): 0.7135768
timestamp: 2017-05-23 13:48:03 
Wall clock time (HH:MM:SS.hh): 00:00:01.26 
optimizer:  CSOLNP 
OpenMx version number: 2.7.11 
Need help?  See help(mxSummary) 
 
> 

Server

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 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.
 
  Natural language support but running in an English locale
 
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.
 
> require(OpenMx)
Loading required package: OpenMx
To take full advantage of multiple cores, use:
  mxOption(NULL, 'Number of Threads', parallel::detectCores())
> data(demoOneFactor)
> factorModel <- mxModel("One Factor",
+       mxMatrix("Full", 5, 1, values=0.8,
+            free=TRUE, name="A"),
+       mxMatrix("Symm", 1, 1, values=1,
+            free=FALSE, name="L"),
+       mxMatrix("Diag", 5, 5, values=1,
+            free=TRUE, name="U"),
+       mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+       mxExpectationNormal(covariance = "R",
+             dimnames = names(demoOneFactor)),
+       mxFitFunctionML(),
+       mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorModelFit <- mxRun(factorModel)
Running One Factor with 10 parameters
Warning message:
In model 'One Factor' Optimizer returned a non-zero status code 6. The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) 
> summary(factorModelFit)
Summary of One Factor 
 
The model does not satisfy the first-order optimality conditions to the required accuracy, and no improved point for the merit function could be found during the final linesearch (Mx status RED) 
 
free parameters:
                name matrix row col Estimate
1  One Factor.A[1,1]      A   1   1       NA
2  One Factor.A[2,1]      A   2   1       NA
3  One Factor.A[3,1]      A   3   1       NA
4  One Factor.A[4,1]      A   4   1       NA
5  One Factor.A[5,1]      A   5   1       NA
6  One Factor.U[1,1]      U   1   1       NA
7  One Factor.U[2,2]      U   2   2       NA
8  One Factor.U[3,3]      U   3   3       NA
9  One Factor.U[4,4]      U   4   4       NA
10 One Factor.U[5,5]      U   5   5       NA
 
Model Statistics: 
               |  Parameters  |  Degrees of Freedom  |  Fit (-2lnL units)
       Model:             10                      5                    NA
   Saturated:             15                      0            -3667.9905
Independence:              5                     10               64.5342
Number of observations/statistics: 500/15
 
Information Criteria: 
      |  df Penalty  |  Parameters Penalty  |  Sample-Size Adjusted
AIC:             NA                     NA                       NA
BIC:             NA                     NA                       NA
To get additional fit indices, see help(mxRefModels)
timestamp: 2017-05-23 13:50:38 
Wall clock time (HH:MM:SS.hh): 00:00:00.62 
optimizer:  CSOLNP 
OpenMx version number: 2.7.11 
Need help?  See help(mxSummary) 
 
> 

Thanks,
Shane

AdminRobK's picture
Offline
Joined: 01/24/2014 - 12:15
maybe there IS a compilation problem
free parameters:
                name matrix row col Estimate
1  One Factor.A[1,1]      A   1   1       NA
2  One Factor.A[2,1]      A   2   1       NA
3  One Factor.A[3,1]      A   3   1       NA
4  One Factor.A[4,1]      A   4   1       NA
5  One Factor.A[5,1]      A   5   1       NA
6  One Factor.U[1,1]      U   1   1       NA
7  One Factor.U[2,2]      U   2   2       NA
8  One Factor.U[3,3]      U   3   3       NA
9  One Factor.U[4,4]      U   4   4       NA
10 One Factor.U[5,5]      U   5   5       NA

Hmm, OK, there definitely seems to be something wrong here.

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