* installing *source* package ‘spAbundance’ ...
** this is package ‘spAbundance’ version ‘0.2.1’
** package ‘spAbundance’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.3 (clang-1403.0.22.14.1)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c DS.cpp -o DS.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c NMix.cpp -o NMix.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c abund.cpp -o abund.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c abundGaussian.cpp -o abundGaussian.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c checkAlphaDS.cpp -o checkAlphaDS.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c checkMSAlphaDS.cpp -o checkMSAlphaDS.o
abundGaussian.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
checkAlphaDS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
DS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
checkMSAlphaDS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
abund.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
NMix.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
DS.cpp:591:51: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
DS.cpp:591:51: note: remove extraneous parentheses around the comparison to silence this warning
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~ ^ ~
DS.cpp:591:51: note: use '=' to turn this equality comparison into an assignment
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
^~
=
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c idist.cpp -o idist.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c init.cpp -o init.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c lfMsAbund.cpp -o lfMsAbund.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c lfMsAbundGaussian.cpp -o lfMsAbundGaussian.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c lfMsDS.cpp -o lfMsDS.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c lfMsNMix.cpp -o lfMsNMix.o
1 warning generated.
lfMsAbund.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c mkSpCov.cpp -o mkSpCov.o
lfMsAbundGaussian.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
lfMsDS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
lfMsNMix.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c msAbund.cpp -o msAbund.o
mkSpCov.cpp:3:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
msAbund.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c msAbundGaussian.cpp -o msAbundGaussian.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c msDS.cpp -o msDS.o
msAbundGaussian.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c msNMix.cpp -o msNMix.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c nn.cpp -o nn.o
msDS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
msNMix.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c rpg.cpp -o rpg.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sfMsAbundGaussianNNGP.cpp -o sfMsAbundGaussianNNGP.o
nn.cpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sfMsAbundNNGP.cpp -o sfMsAbundNNGP.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sfMsAbundNNGPPredict.cpp -o sfMsAbundNNGPPredict.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sfMsDSNNGP.cpp -o sfMsDSNNGP.o
sfMsAbundGaussianNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
sfMsAbundNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
sfMsAbundNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
sfMsDSNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sfMsNMixNNGP.cpp -o sfMsNMixNNGP.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c sfMsNMixNNGPPredict.cpp -o sfMsNMixNNGPPredict.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c spAbundGaussianNNGP.cpp -o spAbundGaussianNNGP.o
sfMsNMixNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
sfMsNMixNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
spAbundGaussianNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c spAbundNNGP.cpp -o spAbundNNGP.o
spAbundNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c spDSNNGP.cpp -o spDSNNGP.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c spNMixNNGP.cpp -o spNMixNNGP.o
spDSNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c spNMixNNGPPredict.cpp -o spNMixNNGPPredict.o
spNMixNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
spNMixNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c svcAbundGaussianNNGP.cpp -o svcAbundGaussianNNGP.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c svcAbundGaussianNNGPPredict.cpp -o svcAbundGaussianNNGPPredict.o
svcAbundGaussianNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
svcAbundGaussianNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c svcAbundNNGP.cpp -o svcAbundNNGP.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c svcAbundNNGPPredict.cpp -o svcAbundNNGPPredict.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c svcMsAbundGaussianNNGP.cpp -o svcMsAbundGaussianNNGP.o
svcAbundNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c svcMsAbundGaussianNNGPPredict.cpp -o svcMsAbundGaussianNNGPPredict.o
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c util.cpp -o util.o
svcAbundNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
svcMsAbundGaussianNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/x86_64/include -fPIC -falign-functions=64 -Wall -g -O2 -DR_NO_REMAP -c waicAbund.cpp -o waicAbund.o
svcMsAbundGaussianNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
util.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
waicAbund.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
#define R_NO_REMAP
^
<command line>:2:9: note: previous definition is here
#define R_NO_REMAP 1
^
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o spAbundance.so DS.o NMix.o abund.o abundGaussian.o checkAlphaDS.o checkMSAlphaDS.o idist.o init.o lfMsAbund.o lfMsAbundGaussian.o lfMsDS.o lfMsNMix.o mkSpCov.o msAbund.o msAbundGaussian.o msDS.o msNMix.o nn.o rpg.o sfMsAbundGaussianNNGP.o sfMsAbundNNGP.o sfMsAbundNNGPPredict.o sfMsDSNNGP.o sfMsNMixNNGP.o sfMsNMixNNGPPredict.o spAbundGaussianNNGP.o spAbundNNGP.o spDSNNGP.o spNMixNNGP.o spNMixNNGPPredict.o svcAbundGaussianNNGP.o svcAbundGaussianNNGPPredict.o svcAbundNNGP.o svcAbundNNGPPredict.o svcMsAbundGaussianNNGP.o svcMsAbundGaussianNNGPPredict.o util.o waicAbund.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.5/spAbundance.Rcheck/00LOCK-spAbundance/00new/spAbundance/libs
** generating debug symbols (dSYM)
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (spAbundance)