* installing *source* package ‘spAbundance’ ...
** 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 -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 -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 -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 -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 -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 -c checkMSAlphaDS.cpp -o checkMSAlphaDS.o
DS.cpp:590:51: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
DS.cpp:590:51: note: remove extraneous parentheses around the comparison to silence this warning
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~ ^ ~
DS.cpp:590:51: note: use '=' to turn this equality comparison into an assignment
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
^~
=
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 -c idist.cpp -o idist.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 -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 -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 -c lfMsAbundGaussian.cpp -o lfMsAbundGaussian.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 -c lfMsDS.cpp -o lfMsDS.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 -c lfMsNMix.cpp -o lfMsNMix.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 -c mkSpCov.cpp -o mkSpCov.o
lfMsDS.cpp:843:53: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
lfMsDS.cpp:843:53: note: remove extraneous parentheses around the comparison to silence this warning
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~ ^ ~
lfMsDS.cpp:843:53: 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 -c msAbund.cpp -o msAbund.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 -c msAbundGaussian.cpp -o msAbundGaussian.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 -c msDS.cpp -o msDS.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 -c msNMix.cpp -o msNMix.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 -c nn.cpp -o nn.o
msDS.cpp:781:53: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
msDS.cpp:781:53: note: remove extraneous parentheses around the comparison to silence this warning
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~ ^ ~
msDS.cpp:781:53: note: use '=' to turn this equality comparison into an assignment
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
^~
=
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 -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 -c sfMsAbundGaussianNNGP.cpp -o sfMsAbundGaussianNNGP.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 -c sfMsAbundNNGP.cpp -o sfMsAbundNNGP.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 -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 -c sfMsDSNNGP.cpp -o sfMsDSNNGP.o
sfMsDSNNGP.cpp:980:53: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
sfMsDSNNGP.cpp:980:53: note: remove extraneous parentheses around the comparison to silence this warning
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~ ^ ~
sfMsDSNNGP.cpp:980:53: 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 -c sfMsNMixNNGP.cpp -o sfMsNMixNNGP.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 -c sfMsNMixNNGPPredict.cpp -o sfMsNMixNNGPPredict.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 -c spAbundGaussianNNGP.cpp -o spAbundGaussianNNGP.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 -c spAbundNNGP.cpp -o spAbundNNGP.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 -c spAbundNNGPPredict.cpp -o spAbundNNGPPredict.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 -c spDSNNGP.cpp -o spDSNNGP.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 -c spNMixNNGP.cpp -o spNMixNNGP.o
spDSNNGP.cpp:731:51: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
spDSNNGP.cpp:731:51: note: remove extraneous parentheses around the comparison to silence this warning
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
~ ^ ~
spDSNNGP.cpp:731:51: note: use '=' to turn this equality comparison into an assignment
if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
^~
=
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 -c spNMixNNGPPredict.cpp -o spNMixNNGPPredict.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 -c svcAbundNNGP.cpp -o svcAbundNNGP.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 -c svcAbundNNGPPredict.cpp -o svcAbundNNGPPredict.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 -c svcMsAbundGaussianNNGP.cpp -o svcMsAbundGaussianNNGP.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 -c svcMsAbundGaussianNNGPPredict.cpp -o svcMsAbundGaussianNNGPPredict.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 -c util.cpp -o util.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 -c waicAbund.cpp -o waicAbund.o
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 spAbundNNGPPredict.o spDSNNGP.o spNMixNNGP.o spNMixNNGPPredict.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-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Volumes/Builds/packages/big-sur-x86_64/results/4.4/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)