* installing *source* package ‘spAbundance’ ...
** package ‘spAbundance’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘clang version 19.1.5’
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/spAbundance/src'
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c DS.cpp -o DS.o
DS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
DS.cpp:591:51: warning: equality comparison with extraneous parentheses [-Wparentheses-equality]
591 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
DS.cpp:591:51: note: remove extraneous parentheses around the comparison to silence this warning
591 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ~ ^ ~
DS.cpp:591:51: note: use '=' to turn this equality comparison into an assignment
591 | if ((XpRE[alphaStarIndx[l] * J + j] == alphaLevelIndx[l])) {
| ^~
| =
2 warnings generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c NMix.cpp -o NMix.o
NMix.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c abund.cpp -o abund.o
abund.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c abundGaussian.cpp -o abundGaussian.o
abundGaussian.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c checkAlphaDS.cpp -o checkAlphaDS.o
checkAlphaDS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c checkMSAlphaDS.cpp -o checkMSAlphaDS.o
checkMSAlphaDS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c idist.cpp -o idist.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c init.cpp -o init.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c lfMsAbund.cpp -o lfMsAbund.o
lfMsAbund.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c lfMsAbundGaussian.cpp -o lfMsAbundGaussian.o
lfMsAbundGaussian.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c lfMsDS.cpp -o lfMsDS.o
lfMsDS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c lfMsNMix.cpp -o lfMsNMix.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c mkSpCov.cpp -o mkSpCov.o
lfMsNMix.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
mkSpCov.cpp:3:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
3 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c msAbund.cpp -o msAbund.o
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c msAbundGaussian.cpp -o msAbundGaussian.o
msAbund.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c msDS.cpp -o msDS.o
msAbundGaussian.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c msNMix.cpp -o msNMix.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c nn.cpp -o nn.o
msDS.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
msNMix.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
nn.cpp:11:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
11 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c rpg.cpp -o rpg.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sfMsAbundGaussianNNGP.cpp -o sfMsAbundGaussianNNGP.o
sfMsAbundGaussianNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sfMsAbundNNGP.cpp -o sfMsAbundNNGP.o
sfMsAbundNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sfMsAbundNNGPPredict.cpp -o sfMsAbundNNGPPredict.o
sfMsAbundNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
9 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sfMsDSNNGP.cpp -o sfMsDSNNGP.o
sfMsDSNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sfMsNMixNNGP.cpp -o sfMsNMixNNGP.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c sfMsNMixNNGPPredict.cpp -o sfMsNMixNNGPPredict.o
sfMsNMixNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
sfMsNMixNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
9 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spAbundGaussianNNGP.cpp -o spAbundGaussianNNGP.o
spAbundGaussianNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spAbundNNGP.cpp -o spAbundNNGP.o
spAbundNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spDSNNGP.cpp -o spDSNNGP.o
spDSNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spNMixNNGP.cpp -o spNMixNNGP.o
spNMixNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c spNMixNNGPPredict.cpp -o spNMixNNGPPredict.o
spNMixNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
9 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c svcAbundGaussianNNGP.cpp -o svcAbundGaussianNNGP.o
svcAbundGaussianNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c svcAbundGaussianNNGPPredict.cpp -o svcAbundGaussianNNGPPredict.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c svcAbundNNGP.cpp -o svcAbundNNGP.o
svcAbundGaussianNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
9 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c svcAbundNNGPPredict.cpp -o svcAbundNNGPPredict.o
svcAbundNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c svcMsAbundGaussianNNGP.cpp -o svcMsAbundGaussianNNGP.o
svcAbundNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
9 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c svcMsAbundGaussianNNGPPredict.cpp -o svcMsAbundGaussianNNGPPredict.o
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c util.cpp -o util.o
svcMsAbundGaussianNNGP.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
svcMsAbundGaussianNNGPPredict.cpp:9:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
9 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
util.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -I"/data/gannet/ripley/R/R-clang/include" -DNDEBUG -isystem /usr/local/clang19/include -I/usr/local/clang/include -fopenmp -fpic -O3 -Wall -pedantic -frtti -Wp,-D_FORTIFY_SOURCE=3 -DR_NO_REMAP -c waicAbund.cpp -o waicAbund.o
1 warning generated.
waicAbund.cpp:10:9: warning: 'R_NO_REMAP' macro redefined [-Wmacro-redefined]
10 | #define R_NO_REMAP
| ^
<command line>:2:9: note: previous definition is here
2 | #define R_NO_REMAP 1
| ^
1 warning generated.
/usr/local/clang19/bin/clang++ -stdlib=libc++ -std=gnu++17 -shared -L/usr/local/clang/lib64 -L/usr/local/clang19/lib -L/usr/local/clang19/lib/x86_64-unknown-linux-gnu -L/usr/local/gcc14/lib64 -L/usr/local/lib64 -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/data/gannet/ripley/R/R-clang/lib -lRlapack -L/data/gannet/ripley/R/R-clang/lib -lRblas -lFortranRuntime -lFortranDecimal -lm -fopenmp
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/spAbundance/src'
make[1]: Entering directory '/data/gannet/ripley/R/packages/tests-clang/spAbundance/src'
make[1]: Leaving directory '/data/gannet/ripley/R/packages/tests-clang/spAbundance/src'
installing to /data/gannet/ripley/R/packages/tests-clang/spAbundance.Rcheck/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)