Install OpenMx on server (Linux 4.14.35-1902.10.8.el7uek.x86_64 #2 SMP with R=3.5.1)

Hi,

I am having trouble installing OpenMx on a Linux server where I don't have admin rights. Here are my the details:

===============================
OS/Software versions
===============================
OS=Linux 4.14.35-1902.10.8.el7uek.x86_64 #2 SMP
conda environment
R=3.5.1
gcc=7.1.0
libgcc=7.2.0

======================
Content of ~/.R/Makevars
=====================
CC = /software/gcc/7.1.0/bin/gcc
CXX = /software/gcc/7.1.0/bin/g++
CXX1X = /software/gcc/7.1.0/bin/g++
FC = /software/gcc/7.1.0/bin/gfortran
F77 = /software/gcc/7.1.0/bin/gfortran

==============================================
Contents of /home/jslim/.conda/envs/qiime2-2019.7/lib/R/etc/Makeconf
==============================================
# etc/Makeconf. Generated from Makeconf.in by configure.
#
# ${R_HOME}/etc/Makeconf
#
# R was configured using the following call
# (not including env. vars and site configuration)
# configure '--prefix=/home/jslim/.conda/envs/qiime2-2019.7' '--host=x86_64-conda_cos6-linux-gnu' '--build=x86_64-conda_cos6-linux-gnu' '--enable-shared' '--enable-R-shlib' '--enable-BLAS-shlib' '--disable-prebuilt-html' '--enable-memory-profiling' '--with-tk-config=/home/jslim/.conda/envs/qiime2-2019.7/lib/tkConfig.sh' '--with-tcl-config=/home/jslim/.conda/envs/qiime2-2019.7/lib/tclConfig.sh' '--with-x' '--with-pic' '--with-cairo' '--with-readline' '--with-recommended-packages=no' '--without-libintl-prefix' 'LIBnn=lib' 'build_alias=x86_64-conda_cos6-linux-gnu' 'host_alias=x86_64-conda_cos6-linux-gnu' 'PKG_CONFIG_PATH=/home/jslim/.conda/envs/qiime2-2019.7/lib/pkgconfig' 'CC=x86_64-conda_cos6-linux-gnu-cc' 'CFLAGS=-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix' 'LDFLAGS=-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/jslim/.conda/envs/qiime2-2019.7/lib -Wl,-rpath-link,/home/jslim/.conda/envs/qiime2-2019.7/lib -L/home/jslim/.conda/envs/qiime2-2019.7/lib -Wl,-rpath-link,/home/jslim/.conda/envs/qiime2-2019.7/lib' 'CPPFLAGS=-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/jslim/.conda/envs/qiime2-2019.7/include -Wl,-rpath-link,/home/jslim/.conda/envs/qiime2-2019.7/lib' 'CPP=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/_build_env/bin/x86_64-conda_cos6-linux-gnu-cpp' 'F77=x86_64-conda_cos6-linux-gnu-gfortran' 'FFLAGS=-fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix' 'CXX=x86_64-conda_cos6-linux-gnu-c++' 'CXXFLAGS=-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix' 'OBJC=x86_64-conda_cos6-linux-gnu-cc' 'FC=x86_64-conda_cos6-linux-gnu-gfortran'

## This fails if it contains spaces, or if it is quoted
include $(R_SHARE_DIR)/make/vars.mk

AR = x86_64-conda_cos6-linux-gnu-ar
BLAS_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRblas
C_VISIBILITY = -fvisibility=hidden
CC = x86_64-conda_cos6-linux-gnu-cc
CFLAGS = -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix $(LTO)
CPICFLAGS = -fpic
CPPFLAGS = -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -I/home/jslim/.conda/envs/qiime2-2019.7/include -Wl,-rpath-link,/home/jslim/.conda/envs/qiime2-2019.7/lib
CXX = x86_64-conda_cos6-linux-gnu-c++
CXXCPP = $(CXX) -E
CXXFLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix $(LTO)
CXXPICFLAGS = -fpic
CXX98 = x86_64-conda_cos6-linux-gnu-c++
CXX98FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix
CXX98PICFLAGS = -fpic
CXX98STD = -std=gnu++98
CXX11 = x86_64-conda_cos6-linux-gnu-c++
CXX11FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix
CXX11PICFLAGS = -fpic
CXX11STD = -std=gnu++11
CXX14 = x86_64-conda_cos6-linux-gnu-c++
CXX14FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix
CXX14PICFLAGS = -fpic
CXX14STD = -std=gnu++14
CXX17 = x86_64-conda_cos6-linux-gnu-c++
CXX17FLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix
CXX17PICFLAGS = -fpic
CXX17STD = -std=gnu++17
DYLIB_EXT = .so
DYLIB_LD = $(CC)
DYLIB_LDFLAGS = -shared -fopenmp# $(CFLAGS) $(CPICFLAGS)
DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS)
ECHO = echo
ECHO_C =
ECHO_N = -n
ECHO_T =
## NB, set FC before F77 as on Solaris make, setting FC sets F77
FC = x86_64-conda_cos6-linux-gnu-gfortran
FCFLAGS = -g -O2 $(LTO)
## additional libs needed when linking with $(FC), e.g. on some Oracle compilers
FCLIBS =
F77 = x86_64-conda_cos6-linux-gnu-gfortran
F77_VISIBILITY = -fvisibility=hidden
FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix $(LTO)
FLIBS = -lgfortran -lm -lgomp -lquadmath -lpthread
FCPICFLAGS = -fpic
FPICFLAGS = -fpic
FOUNDATION_CPPFLAGS =
FOUNDATION_LIBS =
JAR = /home/jslim/.conda/envs/qiime2-2019.7/bin/jar
JAVA = /home/jslim/.conda/envs/qiime2-2019.7/bin/java
JAVAC = /home/jslim/.conda/envs/qiime2-2019.7/bin/javac
JAVAH = /bin/javah
## JAVA_HOME might be used in the next three.
## They are for packages 'JavaGD' and 'rJava'
JAVA_HOME = /home/jslim/.conda/envs/qiime2-2019.7
JAVA_CPPFLAGS = -I$(JAVA_HOME)/include -I$(JAVA_HOME)/include/linux
JAVA_LIBS = -L$(JAVA_HOME)/lib/server -ljvm
JAVA_LD_LIBRARY_PATH = /home/jslim/.conda/envs/qiime2-2019.7/lib/server
LAPACK_LIBS = -L"$(R_HOME)/lib$(R_ARCH)" -lRlapack
## we only need this is if it is external, as otherwise link to R
LIBINTL=
LIBM = -lm
LIBR0 = -L"$(R_HOME)/lib$(R_ARCH)"
LIBR1 = -lR
LIBR = -L"$(R_HOME)/lib$(R_ARCH)" -lR
LIBS = -lpcre -llzma -lbz2 -lz -lrt -ldl -lm -liconv -licuuc -licui18n
## needed by R CMD config
LIBnn = lib
LIBTOOL = $(SHELL) "$(R_HOME)/bin/libtool"
LDFLAGS = -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,-rpath,/home/jslim/.conda/envs/qiime2-2019.7/lib -Wl,-rpath-link,/home/jslim/.conda/envs/qiime2-2019.7/lib -L/home/jslim/.conda/envs/qiime2-2019.7/lib -Wl,-rpath-link,/home/jslim/.conda/envs/qiime2-2019.7/lib
LTO =
## needed to build applications linking to static libR
MAIN_LD = $(CC)
MAIN_LDFLAGS = -Wl,--export-dynamic -fopenmp
RPATH_LDFLAGS = -Wl,-rpath,$(abs_top_builddir)/lib -Wl,-rpath,/home/jslim/.conda/envs/qiime2-2019.7/lib
MAIN_LINK = $(MAIN_LD) $(MAIN_LDFLAGS) $(LDFLAGS) $(RPATH_LDFLAGS)
MKINSTALLDIRS = "$(R_HOME)/bin/mkinstalldirs"
OBJC = x86_64-conda_cos6-linux-gnu-cc
OBJCFLAGS = -g -O2 -fobjc-exceptions $(LTO)
OBJC_LIBS =
OBJCXX =
R_ARCH =
RANLIB = x86_64-conda_cos6-linux-gnu-ranlib
SAFE_FFLAGS = -fopenmp -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix -msse2 -mfpmath=sse
SED = /bin/sed
SHELL = /bin/sh
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = $(CXX)
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX98LD = $(CXX98) $(CXX98STD)
SHLIB_CXX98LDFLAGS = -shared
SHLIB_CXX11LD = $(CXX11) $(CXX11STD)
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = $(CXX14) $(CXX14STD)
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD = $(CXX17) $(CXX17STD)
SHLIB_CXX17LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FCLD = $(FC)
SHLIB_FCLDFLAGS = -shared
SHLIB_FFLAGS =
SHLIB_LD = $(CC)
SHLIB_LDFLAGS = -shared# $(CFLAGS) $(CPICFLAGS)
SHLIB_LIBADD =
## We want to ensure libR is picked up from $(R_HOME)/lib
## before e.g. /usr/local/lib if a version is already installed.
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LIBR0) $(LDFLAGS)
SHLIB_OPENMP_CFLAGS = -fopenmp
SHLIB_OPENMP_CXXFLAGS = -fopenmp
SHLIB_OPENMP_FCFLAGS = -fopenmp
SHLIB_OPENMP_FFLAGS =
STRIP_LIBS = x86_64-conda_cos6-linux-gnu-strip --strip-unneeded
STRIP_STATIC_LIBS = x86_64-conda_cos6-linux-gnu-strip --strip-debug
TCLTK_CPPFLAGS = -I/home/jslim/.conda/envs/qiime2-2019.7/include -I/home/jslim/.conda/envs/qiime2-2019.7/include
TCLTK_LIBS = -L/home/jslim/.conda/envs/qiime2-2019.7/lib -ltcl8.6 -L/home/jslim/.conda/envs/qiime2-2019.7/lib -ltk8.6 -lX11
YACC = yacc

## legacy
CXX1X = x86_64-conda_cos6-linux-gnu-c++
CXX1XFLAGS = -fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -I/home/jslim/.conda/envs/qiime2-2019.7/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/r-base_1562026475051/work=/usr/local/src/conda/r-base-3.5.1 -fdebug-prefix-map=/home/jslim/.conda/envs/qiime2-2019.7=/usr/local/src/conda-prefix
CXX1XPICFLAGS = -fpic
CXX1XSTD = -std=gnu++11
SHLIB_CXX1XLD = $(CXX11) $(CXX11STD)
SHLIB_CXX1XLDFLAGS = -shared

## for linking to libR.a
STATIC_LIBR = # -Wl,--whole-archive "$(R_HOME)/lib$(R_ARCH)/libR.a" -Wl,--no-whole-archive $(BLAS_LIBS) $(FLIBS) $(LIBINTL) -lreadline $(LIBS)

R_XTRA_CFLAGS =
R_XTRA_CPPFLAGS = -I"$(R_INCLUDE_DIR)" -DNDEBUG
R_XTRA_CXXFLAGS =
R_XTRA_FFLAGS =

ALL_CFLAGS = $(R_XTRA_CFLAGS) $(PKG_CFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(CFLAGS)
ALL_CPPFLAGS = $(R_XTRA_CPPFLAGS) $(PKG_CPPFLAGS) $(CLINK_CPPFLAGS) $(CPPFLAGS)
ALL_CXXFLAGS = $(R_XTRA_CXXFLAGS) $(PKG_CXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(CXXFLAGS)
ALL_OBJCFLAGS = $(PKG_OBJCFLAGS) $(CPICFLAGS) $(SHLIB_CFLAGS) $(OBJCFLAGS)
ALL_OBJCXXFLAGS = $(PKG_OBJCXXFLAGS) $(CXXPICFLAGS) $(SHLIB_CXXFLAGS) $(OBJCXXFLAGS)
ALL_FFLAGS = $(R_XTRA_FFLAGS) $(PKG_FFLAGS) $(FPICFLAGS) $(SHLIB_FFLAGS) $(FFLAGS)
## LIBR here as a couple of packages use this without SHLIB_LINK
ALL_LIBS = $(PKG_LIBS) $(SHLIB_LIBADD) $(LIBR)# $(LIBINTL)

.SUFFIXES:
.SUFFIXES: .c .cc .cpp .d .f .f90 .f95 .m .mm .M .o

.c.o:
$(CC) $(ALL_CPPFLAGS) $(ALL_CFLAGS) -c $< -o $@
.c.d:
@echo "making $@ from $<"
@$(CC) -MM $(ALL_CPPFLAGS) $< > $@
.cc.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cpp.o:
$(CXX) $(ALL_CPPFLAGS) $(ALL_CXXFLAGS) -c $< -o $@
.cc.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.cpp.d:
@echo "making $@ from $<"
@$(CXX) -M $(ALL_CPPFLAGS) $< > $@
.m.o:
$(OBJC) $(ALL_CPPFLAGS) $(ALL_OBJCFLAGS) -c $< -o $@
.m.d:
@echo "making $@ from $<"
@x86_64-conda_cos6-linux-gnu-cc -MM $(ALL_CPPFLAGS) $< > $@
.mm.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.M.o:
$(OBJCXX) $(ALL_CPPFLAGS) $(ALL_OBJCXXFLAGS) -c $< -o $@
.f.o:
$(F77) $(ALL_FFLAGS) -c $< -o $@
.f95.o:
$(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $< -o $@
.f90.o:
$(FC) $(PKG_FCFLAGS) $(FCPICFLAGS) $(FCFLAGS) -c $< -o $@

=============================================
Installation log and errors
=============================================
options(repos="https://cran.rstudio.com/")

./configure --prefix=$HOME/software/packages

~/.R/Makevars

CC = /software/gcc/7.1.0/bin/gcc
CXX = /software/gcc/7.1.0/bin/g++
CXX1X = /software/gcc/7.1.0/bin/g++
FC = /software/gcc/7.1.0/bin/gfortran
F77 = /software/gcc/7.1.0/bin/gfortran

src/libnpsol.a

OS=Linux 4.14.35-1902.10.8.el7uek.x86_64 #2 SMP
conda environment
R=3.5.1
gcc=7.1.0
libgcc=7.2.0
===

/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/products/Selfadjoin
tMatrixVector.h: In instantiation of 'static void Eigen::internal::selfadjoint_matrix_vector_product<Scalar, Index, StorageOrder, UpLo, ConjugateLhs, ConjugateRhs, Version>::run(Index, const Scalar*, Index, const Scalar*, Scalar*, Scalar) [with Scalar = double; Index = int; int StorageOrder = 0; int UpLo = 2; b
ool ConjugateLhs = false; bool ConjugateRhs = false; int Version = 0]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/products/Selfadjoin
tMatrixVector.h:227:7: required from 'static void Eigen::internal::selfadjoint_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::run(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >; int LhsMode = 18; Rhs = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Eigen::internal::selfadjoint
_product_impl<Lhs, LhsMode, false, Rhs, 0, true>::Scalar = double]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h
:746:109: required from 'static void Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::SelfAdjointShape, Eigen::DenseShape, ProductTag>::scaleAndAddTo(Dest&, const Lhs&, const Rhs&, const Scalar&) [with Dest = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>; Rhs = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; int ProductTag = 7; Eigen::internal::generic_product_impl<Lhs, Rhs, Eigen::SelfAdjointShape, Eigen:
:DenseShape, ProductTag>::Scalar = double]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h
:361:27: required from 'static void Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::scaleAndAddTo(Dst&, const Lhs&, const Rhs&, const Scalar&) [with Dst = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>; Rhs = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Derived = Eigen::internal::generic_product_impl<Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>, Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::SelfAdjointShape, Eigen::DenseS
hape, 7>; Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::Scalar = double]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h
:349:33: required from 'static void Eigen::internal::generic_product_impl_base<Lhs, Rhs, Derived>::evalTo(Dst&, const Lhs&, const Rhs&) [with Dst = Eigen::Matrix<double, -1, 1>; Lhs = Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>; Rhs = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Derived = Eigen::internal::generic_product_impl<Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>, Eigen::Map<Eigen::Matri
x<double, -1, 1>, 0, Eigen::Stride<0, 0> >, Eigen::SelfAdjointShape, Eigen::DenseShape, 7>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h
:124:75: required from 'Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, Option>, ProductTag, LhsShape, RhsShape>::product_evaluator(const XprType&) [with Lhs = Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>; Rhs = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; int Options = 0; int ProductTag = 7; LhsShape = Eigen::SelfAdjointShape; RhsShape = Eigen::DenseShape; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, Option>::Rhs>::Scalar = double; typename Eigen::internal::traits<typename Eigen::Product<Lhs, Rhs, Option>::Lhs>::Scalar = double; Eigen::internal::product_evaluator<Eigen::Product<Lhs, Rhs, Option>, ProductTag, LhsShape, RhsShape>::XprType = Eigen::Product<Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1
>, 0, Eigen::Stride<0, 0> >, 2>, Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, 0>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h
:35:90: [ skipping 11 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:8
79:31: required from 'static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; SrcXprType = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Product<Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>, Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, 0> > >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> > >; Functor = Eigen::internal::assign_op<double, double>; Weak = voi
d]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:8
36:49: required from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Product<Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>, Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, 0> > >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<do
uble>, const Eigen::Array<double, -1, 1> > >; Func = Eigen::internal::assign_op<double, double>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:8
04:27: required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if<(! Eigen::internal::evaluator_assume_aliasing<Src>::value), void*>::type) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Product<Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>, Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, 0> > >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> > >; Func = Eigen::internal::assign_op<double, double>; typename Eigen::internal::enable_if<(! Eigen::internal::evaluator_assume_aliasing<Src>::value), void*>::type = voi
d*]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:7
82:18: required from 'void Eigen::internal::call_assignment(Dst&, const Src&) [with Dst = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Src = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Product<Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>, Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, 0> > >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Ar
ray<double, -1, 1> > >]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Assign.h:66:28: r
equired from 'Derived& Eigen::MatrixBase<Derived>::operator=(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_sum_op<double, double>, const Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> >, const Eigen::ArrayWrapper<const Eigen::Product<Eigen::SelfAdjointView<Eigen::Map<Eigen::Matrix<double, -1, -1>, 0, Eigen::Stride<0, 0> >, 2>, Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >, 0> > >, const Eigen::CwiseNullaryOp<Eigen::internal::scalar_constant_op<double>, const Eigen::Array<double, -1, 1> > >; Derived = Eigen::Map
<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >]'
omxMatrix.h:442:86: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/products/Selfadjoin
tMatrixVector.h:60:121: warning: ignoring attributes on template argument 'Eigen::internal::packet_trait
s<double>::type {aka __vector(2) double}' [-Wignored-attributes]
:IsComplex && EIGEN_LOGICAL_XOR(ConjugateLhs, IsRowMajor), ConjugateRhs> pcj0;
^~~~
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/products/Selfadjoin
tMatrixVector.h:60:121: warning: ignoring attributes on template argument 'Eigen::internal::packet_trait
s<double>::type {aka __vector(2) double}' [-Wignored-attributes]
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/products/Selfadjoin
tMatrixVector.h:61:121: warning: ignoring attributes on template argument 'Eigen::internal::packet_trait
s<double>::type {aka __vector(2) double}' [-Wignored-attributes]
:IsComplex && EIGEN_LOGICAL_XOR(ConjugateLhs, !IsRowMajor), ConjugateRhs> pcj1;
^~~~
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/products/Selfadjoin
tMatrixVector.h:61:121: warning: ignoring attributes on template argument 'Eigen::internal::packet_trait
s<double>::type {aka __vector(2) double}' [-Wignored-attributes]
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/Core:4
40:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/Dense:
1,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
prim/mat/fun/Eigen.hpp:4,
from omxDefines.h:233,
from omxMLFitFunction.cpp:17:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h: I
n instantiation of 'struct Eigen::internal::evaluator<Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1,
true> >':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:7
30:20: required from 'void Eigen::internal::call_dense_assignment_loop(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, true>; SrcXprType = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, true>; Functor = Eigen::internal::swap_assign_op<dou
ble>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:8
79:31: required from 'static void Eigen::internal::Assignment<DstXprType, SrcXprType, Functor, Eigen::internal::Dense2Dense, Weak>::run(DstXprType&, const SrcXprType&, const Functor&) [with DstXprType = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, true>; SrcXprType = Eigen::Block<Eigen::Matrix<double, -1
, 1>, -1, 1, true>; Functor = Eigen::internal::swap_assign_op<double>; Weak = void]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:8
36:49: required from 'void Eigen::internal::call_assignment_no_alias(Dst&, const Src&, const Func&) [with Dst = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, true>; Src = Eigen::Block<Eigen::Matrix<doub
le, -1, 1>, -1, 1, true>; Func = Eigen::internal::swap_assign_op<double>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/AssignEvaluator.h:8
04:27: required from 'void Eigen::internal::call_assignment(Dst&, const Src&, const Func&, typename Eigen::internal::enable_if<(! Eigen::internal::evaluator_assume_aliasing<Src>::value), void*>::type) [with Dst = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, true>; Src = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, true>; Func = Eigen::internal::swap_assign_op<double>; typename Eigen::internal::enable_
if<(! Eigen::internal::evaluator_assume_aliasing<Src>::value), void*>::type = void*]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:418:22:
required from 'void Eigen::DenseBase<Derived>::swap(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Block<Eigen::Matrix<double, -1, 1>, -1, 1, true>; Derived = Eigen::Block<Eigen::Matrix
<double, -1, 1>, -1, 1, true>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/ProductEvaluators.h
:1062:36: [ skipping 12 instantiation contexts, use -ftemplate-backtrace-limit=0 to disable ]
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/PlainObjectBase.h:5
37:19: required from 'Eigen::PlainObjectBase<Derived>::PlainObjectBase(const Eigen::DenseBase<OtherDerived>&) [with OtherDerived = Eigen::Solve<Eigen::LDLT<Eigen::Matrix<double, -1, -1>, 1>, Eigen::Matrix<d
ouble, -1, 1> >; Derived = Eigen::Matrix<double, -1, 1>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Matrix.h:377:29:
required from 'Eigen::Matrix<_Scalar, _Rows, _Cols, _Options, _MaxRows, _MaxCols>::Matrix(const Eigen::EigenBase<OtherDerived>&) [with OtherDerived = Eigen::Solve<Eigen::LDLT<Eigen::Matrix<double, -1, -1>, 1>, Eigen::Matrix<double, -1, 1> >; _Scalar = double; int _Rows = -1; int _Cols = 1; int _Options = 0; int
_MaxRows = -1; int _MaxCols = 1]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/mdivide_l
eft_ldlt.hpp:30:79: required from 'Eigen::Matrix<typename boost::math::tools::promote_args<T1, T2>::type, R1, C2> stan::math::mdivide_left_ldlt(const stan::math::LDLT_factor<T1, R1, C1>&, const Eigen::Matrix<T2, R2, C2>&) [with int R1 = -1; int C1 = -1; int R2 = -1; int C2 = 1; T1 = double; T2 = double; typen
ame boost::math::tools::promote_args<T1, T2>::type = double]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/prim/mat/fun/trace_inv
_quad_form_ldlt.hpp:29:56: required from 'typename std::enable_if<((! stan::is_var<T>::value) && (! stan::is_var<T2>::value)), typename boost::math::tools::promote_args<RT1, RT2>::type>::type stan::math::trace_inv_quad_form_ldlt(const stan::math::LDLT_factor<T1, R2, C2>&, const Eigen::Matrix<T2, R2, C2>&) [with T1 = double; T2 = double; int R2 = -1; int C2 = -1; int R3 = -1; int C3 = 1; typename std::enable_if<((! stan::is_var<T>::value) && (! stan::is_var<T2>::value)), typename boost::math::tools::promote_args<R
T1, RT2>::type>::type = double]'
multi_normal_sufficient.hpp:83:32: required from 'typename boost::math::tools::promote_args<T_sample, typename stan::scalar_type<T_high>::type, T_covar>::type stan::prob::multi_normal_sufficient_log(int, const Eigen::Matrix<RhsScalar, -1, 1>&, const Eigen::Matrix<S, -1, -1>&, const T_loc&, const Eigen::Matrix<T_G, -1, -1>&) [with bool propto = false; T_sample = double; T_loc = Eigen::Matrix<double, -1, 1>; T_covar = double; typename boost::math::tools::promote_args<T_sample, typename stan::scalar_type<T_high>::ty
pe, T_covar>::type = double]'
omxMLFitFunction.cpp:173:96: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/CoreEvaluators.h:96
0:8: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type {ak
a __vector(2) double}' [-Wignored-attributes]
enum {
^
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat/fun/ordered_constrain.hpp:6:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat.hpp:41,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:6,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp: In instantiation of 'constexpr auto stan::math::internal::apply_impl(const F&, const Tuple&, std::index_sequence<_Idx ...>) [with F = stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::math::internal::softmax_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]::<lambda(auto:1&& ...)>; Tuple = std::tuple<Eigen::Matrix<double, -1, 1, 0, -1, 1> >; long unsigned int ...I = {0}; std::i
ndex_sequence<_Idx ...> = std::integer_sequence<long unsigned int, 0>]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:49:20: required from 'constexpr auto stan::math::internal::apply(const F&, const Tuple&) [with F = stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::math::internal::softmax_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]::<lambda(auto:1&& ...)>; Tuple = std::tuple<Eigen::M
atrix<double, -1, 1, 0, -1, 1> >]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:535:20: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::softmax_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:31:53: warning: unused parameter 'i' [-Wunused-parameter]
std::index_sequence<I...> i) {
^
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat.hpp:48:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:6,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_co
nstrain.hpp: In instantiation of 'auto stan::math::internal::simplex_constrain_op::multiply_adjoint_jacobian(const std::array<bool, size>&, const VectorXd&) const [with long unsigned int size = 1; Eigen::Vect
orXd = Eigen::Matrix<double, -1, 1>]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:533:10: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::simplex_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/simplex_co
nstrain.hpp:66:64: warning: unused parameter 'needs_adj' [-Wunused-parameter]
auto multiply_adjoint_jacobian(const std::array<bool, size>& needs_adj,
^~~~~~~~~
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat/fun/ordered_constrain.hpp:6:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat.hpp:41,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:6,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp: In instantiation of 'constexpr auto stan::math::internal::apply_impl(const F&, const Tuple&, std::index_sequence<_Idx ...>) [with F = stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::math::internal::simplex_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]::<lambda(auto:1&& ...)>; Tuple = std::tuple<Eigen::Matrix<double, -1, 1, 0, -1, 1> >; long unsigned int ...I = {
0}; std::index_sequence<_Idx ...> = std::integer_sequence<long unsigned int, 0>]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:49:20: required from 'constexpr auto stan::math::internal::apply(const F&, const Tuple&) [with F = stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::math::internal::simplex_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]::<lambda(auto:1&& ...)>; Tuple = std::tupl
e<Eigen::Matrix<double, -1, 1, 0, -1, 1> >]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:535:20: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::simplex_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:31:53: warning: unused parameter 'i' [-Wunused-parameter]
std::index_sequence<I...> i) {
^
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat.hpp:42:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:6,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/positive_o
rdered_constrain.hpp: In instantiation of 'auto stan::math::internal::positive_ordered_constrain_op::multiply_adjoint_jacobian(const std::array<bool, size>&, const VectorXd&) const [with long unsigned int siz
e = 1; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:533:10: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::positive_ordered_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/positive_o
rdered_constrain.hpp:61:64: warning: unused parameter 'needs_adj' [-Wunused-parameter]
auto multiply_adjoint_jacobian(const std::array<bool, size>& needs_adj,
^~~~~~~~~
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat/fun/ordered_constrain.hpp:6:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat.hpp:41,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:6,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp: In instantiation of 'constexpr auto stan::math::internal::apply_impl(const F&, const Tuple&, std::index_sequence<_Idx ...>) [with F = stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::math::internal::positive_ordered_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]::<lambda(auto:1&& ...)>; Tuple = std::tuple<Eigen::Matrix<double, -1, 1, 0, -1, 1> >; long unsigned int
...I = {0}; std::index_sequence<_Idx ...> = std::integer_sequence<long unsigned int, 0>]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:49:20: required from 'constexpr auto stan::math::internal::apply(const F&, const Tuple&) [with F = stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::math::internal::positive_ordered_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]::<lambda(auto:1&& ...)>; Tuple =
std::tuple<Eigen::Matrix<double, -1, 1, 0, -1, 1> >]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:535:20: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::positive_ordered_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:31:53: warning: unused parameter 'i' [-Wunused-parameter]
std::index_sequence<I...> i) {
^
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat.hpp:41:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:6,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_co
nstrain.hpp: In instantiation of 'auto stan::math::internal::ordered_constrain_op::multiply_adjoint_jacobian(const std::array<bool, size>&, const VectorXd&) const [with long unsigned int size = 1; Eigen::Vect
orXd = Eigen::Matrix<double, -1, 1>]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:533:10: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::ordered_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/ordered_co
nstrain.hpp:60:64: warning: unused parameter 'needs_adj' [-Wunused-parameter]
auto multiply_adjoint_jacobian(const std::array<bool, size>& needs_adj,
^~~~~~~~~
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat/fun/ordered_constrain.hpp:6:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat.hpp:41,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:6,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp: In instantiation of 'constexpr auto stan::math::internal::apply_impl(const F&, const Tuple&, std::index_sequence<_Idx ...>) [with F = stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::math::internal::ordered_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]::<lambda(auto:1&& ...)>; Tuple = std::tuple<Eigen::Matrix<double, -1, 1, 0, -1, 1> >; long unsigned int ...I = {
0}; std::index_sequence<_Idx ...> = std::integer_sequence<long unsigned int, 0>]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:49:20: required from 'constexpr auto stan::math::internal::apply(const F&, const Tuple&) [with F = stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::math::internal::ordered_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]::<lambda(auto:1&& ...)>; Tuple = std::tupl
e<Eigen::Matrix<double, -1, 1, 0, -1, 1> >]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:535:20: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::ordered_constrain_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:31:53: warning: unused parameter 'i' [-Wunused-parameter]
std::index_sequence<I...> i) {
^
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/mat.hpp:49:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:6,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/softmax.hp
p: In instantiation of 'std::tuple<Eigen::Matrix<double, -1, 1, 0, -1, 1> > stan::math::internal::softmax_op::multiply_adjoint_jacobian(const std::array<bool, size>&, const VectorXd&) const [with long unsigne
d int size = 1; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:533:10: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::softmax_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/softmax.hp
p:51:37: warning: unused parameter 'needs_adj' [-Wunused-parameter]
const std::array<bool, size>& needs_adj,
^~~~~~~~~
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/Core:4
34:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/Dense:
1,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
prim/mat/fun/Eigen.hpp:4,
from omxDefines.h:233,
from omxMLFitFunction.cpp:17:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:
In instantiation of 'class Eigen::DenseCoeffsBase<Eigen::CwiseBinaryOp<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1
>, 0, Eigen::Stride<0, 0> > >, 0>':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseBase.h:41:34:
required from 'class Eigen::DenseBase<Eigen::CwiseBinaryOp<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eige
n::Stride<0, 0> > > >'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/MatrixBase.h:48:34:
required from 'class Eigen::MatrixBase<Eigen::CwiseBinaryOp<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Ei
gen::Stride<0, 0> > > >'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:148
:7: required from 'class Eigen::CwiseBinaryOpImpl<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride
<0, 0> >, Eigen::Dense>'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/CwiseBinaryOp.h:77:
7: required from 'class Eigen::CwiseBinaryOp<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0
> > >'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Dot.h:37:48: requ
ired from 'static Eigen::internal::dot_nocheck<T, U, NeedToTranspose>::ResScalar Eigen::internal::dot_nocheck<T, U, NeedToTranspose>::run(const Eigen::MatrixBase<Derived>&, const Eigen::MatrixBase<U>&) [with T = Eigen::Matrix<double, -1, 1>; U = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >;
bool NeedToTranspose = false; Eigen::internal::dot_nocheck<T, U, NeedToTranspose>::ResScalar = double]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Dot.h:84:58: requ
ired from 'typename Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>::ReturnType Eigen::MatrixBase<Derived>::dot(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Derived = Eigen::Matrix<double, -1, 1>; typename Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>::ReturnType = d
ouble]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/softmax.hp
p:56:31: required from 'std::tuple<Eigen::Matrix<double, -1, 1, 0, -1, 1> > stan::math::internal::softmax_op::multiply_adjoint_jacobian(const std::array<bool, size>&, const VectorXd&) const [with long unsig
ned int size = 1; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:533:10: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::softmax_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:5
5:30: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type {a
ka __vector(2) double}' [-Wignored-attributes]
>::type PacketReturnType;
^~~~~~~~~~~~~~~~
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:
In instantiation of 'Eigen::Index Eigen::internal::first_default_aligned(const Eigen::DenseBase<Derived>&) [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >;
Eigen::Index = int]':
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:225:63: r
equired from 'static Eigen::internal::redux_impl<Func, Derived, 3, 0>::Scalar Eigen::internal::redux_impl<Func, Derived, 3, 0>::run(const Derived&, const Func&) [with Func = Eigen::internal::scalar_sum_op<double, double>; Derived = Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > > >; Eigen::internal::redux_impl<Func, Derived, 3, 0>::Scalar = doubl
e]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:418:56: r
equired from 'typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<double, double>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >; typename Eigen::internal::traits<T>::Scala
r = double]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Redux.h:453:73: r
equired from 'typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::sum() const [with Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_conj_product_op<double, double>, const Eigen::Matrix<double, -1, 1>, const Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> > >; typename E
igen::internal::traits<T>::Scalar = double]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Dot.h:37:52: requ
ired from 'static Eigen::internal::dot_nocheck<T, U, NeedToTranspose>::ResScalar Eigen::internal::dot_nocheck<T, U, NeedToTranspose>::run(const Eigen::MatrixBase<Derived>&, const Eigen::MatrixBase<U>&) [with T = Eigen::Matrix<double, -1, 1>; U = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >;
bool NeedToTranspose = false; Eigen::internal::dot_nocheck<T, U, NeedToTranspose>::ResScalar = double]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/Dot.h:84:58: requ
ired from 'typename Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>::ReturnType Eigen::MatrixBase<Derived>::dot(const Eigen::MatrixBase<OtherDerived>&) const [with OtherDerived = Eigen::Map<Eigen::Matrix<double, -1, 1>, 0, Eigen::Stride<0, 0> >; Derived = Eigen::Matrix<double, -1, 1>; typename Eigen::ScalarBinaryOpTraits<typename Eigen::internal::traits<T>::Scalar, typename Eigen::internal::traits<OtherDerived>::Scalar>::ReturnType = d
ouble]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/fun/softmax.hp
p:56:31: required from 'std::tuple<Eigen::Matrix<double, -1, 1, 0, -1, 1> > stan::math::internal::softmax_op::multiply_adjoint_jacobian(const std::array<bool, size>&, const VectorXd&) const [with long unsig
ned int size = 1; Eigen::VectorXd = Eigen::Matrix<double, -1, 1>]'
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/mat/functor/adj_ja
c_apply.hpp:533:10: required from 'void stan::math::adj_jac_vari<F, Targs>::chain() [with F = stan::ma
th::internal::softmax_op; Targs = {Eigen::Matrix<stan::math::var, -1, 1, 0, -1, 1>}]'
omxMLFitFunction.cpp:455:1: required from here
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/RcppEigen/include/Eigen/src/Core/DenseCoeffsBase.h:6
50:34: warning: ignoring attributes on template argument 'Eigen::internal::packet_traits<double>::type {
aka __vector(2) double}' [-Wignored-attributes]
return internal::first_aligned<int(unpacket_traits<DefaultPacketType>::alignment),Derived>(m);
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/core.hpp:46:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat/fun/typedefs.hpp:6,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:4,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_
adjoints_nested.hpp: At global scope:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_
adjoints_nested.hpp:17:13: warning: 'void stan::math::set_zero_all_adjoints_nested()' defined but not us
ed [-Wunused-function]
static void set_zero_all_adjoints_nested() {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
rev/core.hpp:45:0,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat/fun/typedefs.hpp:6,
from /home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/
mix/mat.hpp:4,
from omxMLFitFunction.cpp:20:
/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/StanHeaders/include/stan/math/rev/core/set_zero_all_
adjoints.hpp:14:13: warning: 'void stan::math::set_zero_all_adjoints()' defined but not used [-Wunused-f
unction]
static void set_zero_all_adjoints() {
^~~~~~~~~~~~~~~~~~~~~
make: *** [/home/jslim/.conda/envs/qiime2-2019.7/lib/R/etc/Makeconf:167: omxMLFitFunction.o] Error 1
ERROR: compilation failed for package âOpenMxâ
* removing â/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/OpenMxâ
* restoring previous â/home/jslim/.conda/envs/qiime2-2019.7/lib/R/library/OpenMxâ

The downloaded source packages are in
â/local_scratch/pbs.8718542.pbs02/RtmpkaKRM1/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("OpenMx") :
installation of package âOpenMxâ had non-zero exit status