* installing to library ‘/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages’
* installing *source* package ‘spAbundance’ ...
** package ‘spAbundance’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘Debian clang version 18.1.4 (1)’
make[1]: Entering directory '/tmp/RtmppLxMho/R.INSTALL1fd20263aa5f7d/spAbundance/src'
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c DS.cpp -o DS.o
DS.cpp:590:51: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
590 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
DS.cpp:590:51: note: remove extraneous parentheses around the comparison to silence this warning
590 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~ ^ ~
DS.cpp:590:51: note: use '=' to turn this equality comparison into an assignment
590 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ^~
| =
1 warning generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c NMix.cpp -o NMix.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c abund.cpp -o abund.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c abundGaussian.cpp -o abundGaussian.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c checkAlphaDS.cpp -o checkAlphaDS.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c checkMSAlphaDS.cpp -o checkMSAlphaDS.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c idist.cpp -o idist.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c init.cpp -o init.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c lfMsAbund.cpp -o lfMsAbund.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c lfMsAbundGaussian.cpp -o lfMsAbundGaussian.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c lfMsDS.cpp -o lfMsDS.o
lfMsDS.cpp:843:53: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
843 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
lfMsDS.cpp:843:53: note: remove extraneous parentheses around the comparison to silence this warning
843 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~ ^ ~
lfMsDS.cpp:843:53: note: use '=' to turn this equality comparison into an assignment
843 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ^~
| =
1 warning generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c lfMsNMix.cpp -o lfMsNMix.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c mkSpCov.cpp -o mkSpCov.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c msAbund.cpp -o msAbund.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c msAbundGaussian.cpp -o msAbundGaussian.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c msDS.cpp -o msDS.o
msDS.cpp:781:53: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
781 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
msDS.cpp:781:53: note: remove extraneous parentheses around the comparison to silence this warning
781 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~ ^ ~
msDS.cpp:781:53: note: use '=' to turn this equality comparison into an assignment
781 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ^~
| =
1 warning generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c msNMix.cpp -o msNMix.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c nn.cpp -o nn.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c rpg.cpp -o rpg.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sfMsAbundGaussianNNGP.cpp -o sfMsAbundGaussianNNGP.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sfMsAbundNNGP.cpp -o sfMsAbundNNGP.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sfMsAbundNNGPPredict.cpp -o sfMsAbundNNGPPredict.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sfMsDSNNGP.cpp -o sfMsDSNNGP.o
sfMsDSNNGP.cpp:980:53: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
980 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
sfMsDSNNGP.cpp:980:53: note: remove extraneous parentheses around the comparison to silence this warning
980 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~ ^ ~
sfMsDSNNGP.cpp:980:53: note: use '=' to turn this equality comparison into an assignment
980 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ^~
| =
1 warning generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sfMsNMixNNGP.cpp -o sfMsNMixNNGP.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c sfMsNMixNNGPPredict.cpp -o sfMsNMixNNGPPredict.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c spAbundGaussianNNGP.cpp -o spAbundGaussianNNGP.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c spAbundNNGP.cpp -o spAbundNNGP.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c spAbundNNGPPredict.cpp -o spAbundNNGPPredict.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c spDSNNGP.cpp -o spDSNNGP.o
spDSNNGP.cpp:731:51: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
731 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
spDSNNGP.cpp:731:51: note: remove extraneous parentheses around the comparison to silence this warning
731 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~ ^ ~
spDSNNGP.cpp:731:51: note: use '=' to turn this equality comparison into an assignment
731 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ^~
| =
1 warning generated.
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c spNMixNNGP.cpp -o spNMixNNGP.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c spNMixNNGPPredict.cpp -o spNMixNNGPPredict.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c svcAbundNNGP.cpp -o svcAbundNNGP.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c svcAbundNNGPPredict.cpp -o svcAbundNNGPPredict.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c svcMsAbundGaussianNNGP.cpp -o svcMsAbundGaussianNNGP.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c svcMsAbundGaussianNNGPPredict.cpp -o svcMsAbundGaussianNNGPPredict.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c util.cpp -o util.o
clang++-18 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O3 -Wall -pedantic -c waicAbund.cpp -o waicAbund.o
clang++-18 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -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 -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/llvm-18/lib -lFortran_main -lFortranRuntime -lFortranDecimal -lm -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmppLxMho/R.INSTALL1fd20263aa5f7d/spAbundance/src'
make[1]: Entering directory '/tmp/RtmppLxMho/R.INSTALL1fd20263aa5f7d/spAbundance/src'
make[1]: Leaving directory '/tmp/RtmppLxMho/R.INSTALL1fd20263aa5f7d/spAbundance/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-spAbundance/00new/spAbundance/libs
** 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)