* installing to library ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages’
* installing *source* package ‘Morpho’ ...
** package ‘Morpho’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc-13 (Debian 13.2.0-23) 13.2.0’
using C++ compiler: ‘g++-13 (Debian 13.2.0-23) 13.2.0’
make[1]: Entering directory '/tmp/RtmparJ1dU/R.INSTALL11f91a3619903c/Morpho/src'
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c CVAdists.cpp -o CVAdists.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c CubeStuff.cpp -o CubeStuff.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c ang_calc.cpp -o ang_calc.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from doozers.h:7,
from ang_calc.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’
329 | #pragma message ("INFO: see the documentation for details")
| ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c armaGinvCpp.cpp -o armaGinvCpp.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c asymPerm.cpp -o asymPerm.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c barycenter.cpp -o barycenter.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c covPCA.cpp -o covPCA.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from covPCA.h:5,
from covPCA.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’
329 | #pragma message ("INFO: see the documentation for details")
| ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c createL.cpp -o createL.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c doozers.cpp -o doozers.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c edgePlane.cpp -o edgePlane.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from doozers.h:7,
from edgePlane.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’
329 | #pragma message ("INFO: see the documentation for details")
| ^
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c face_zero.cpp -o face_zero.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c fastSubsetMeans.cpp -o fastSubsetMeans.o
fastSubsetMeans.cpp: In function ‘SEXPREC* fastSubsetMeans(SEXP, SEXP, SEXP, SEXP)’:
fastSubsetMeans.cpp:22:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘unsigned int’} [-Wsign-compare]
22 | for (int j = 0; j < tmpinds.size();j++)
| ~~^~~~~~~~~~~~~~~~
gcc-13 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fpic -g -O2 -Wall -Wstrict-prototypes -pedantic -mtune=native -c init.c -o init.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c meshres.cpp -o meshres.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c permudistArma.cpp -o permudistArma.o
permudistArma.cpp: In function ‘SEXPREC* permudistArma(SEXP, SEXP, SEXP, SEXP)’:
permudistArma.cpp:9:10: warning: unused variable ‘usemedian’ [-Wunused-variable]
9 | bool usemedian = Rcpp::as<bool>(usemedian_);
| ^~~~~~~~~
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c points2mesh.cpp -o points2mesh.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tpsfx.cpp -o tpsfx.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c tweakU.cpp -o tweakU.o
g++-13 -std=gnu++17 -I"/home/hornik/tmp/R.check/r-patched-gcc/Work/build/include" -DNDEBUG -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/Rcpp/include' -I'/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include' -I/usr/local/include -D_FORTIFY_SOURCE=3 -fopenmp -fpic -g -O2 -Wall -pedantic -mtune=native -c updateNormals.cpp -o updateNormals.o
In file included from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo:26,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo/interface/RcppArmadilloForward.h:57,
from /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/RcppArmadillo.h:29,
from doozers.h:7,
from updateNormals.h:4,
from updateNormals.cpp:1:
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:321:86: note: ‘#pragma message: INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed’
321 | #pragma message ("INFO: support for ARMA_DONT_PRINT_ERRORS option has been removed")
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:326:75: note: ‘#pragma message: INFO: suggest to use ARMA_WARN_LEVEL option instead’
326 | #pragma message ("INFO: suggest to use ARMA_WARN_LEVEL option instead")
| ^
/home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/RcppArmadillo/include/armadillo_bits/config.hpp:329:61: note: ‘#pragma message: INFO: see the documentation for details’
329 | #pragma message ("INFO: see the documentation for details")
| ^
g++-13 -std=gnu++17 -shared -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -Wl,-O1 -o Morpho.so CVAdists.o CubeStuff.o ang_calc.o armaGinvCpp.o asymPerm.o barycenter.o covPCA.o createL.o doozers.o edgePlane.o face_zero.o fastSubsetMeans.o init.o meshres.o permudistArma.o points2mesh.o tpsfx.o tweakU.o updateNormals.o -llapack -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/hornik/tmp/R.check/r-patched-gcc/Work/build/lib -lR
make[1]: Leaving directory '/tmp/RtmparJ1dU/R.INSTALL11f91a3619903c/Morpho/src'
make[1]: Entering directory '/tmp/RtmparJ1dU/R.INSTALL11f91a3619903c/Morpho/src'
make[1]: Leaving directory '/tmp/RtmparJ1dU/R.INSTALL11f91a3619903c/Morpho/src'
installing to /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/00LOCK-Morpho/00new/Morpho/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘Morpho’
finding HTML links ... done
CAC html
CVA html
CreateL html
LPS2RAS html
Morpho-deprecated html
Morpho-package html
NNshapeReg html
PCdist html
ProcGPA html
RegScore html
align2procSym html
angle.calc html
angleTest html
anonymize html
applyTransform html
areaSphere html
areaSpherePart html
armaGinv html
arrMean3 html
array2list html
asymPermute html
barycenter html
bindArr html
boneData html
cExtract html
cSize html
checkLM html
checkNA html
classify html
closemeshKD html
colors html
computeArea html
computeTransform html
covDist html
covW html
createAtlas html
createMissingList html
cutMeshPlane html
cutSpace html
data2platonic html
deformGrid2d html
deformGrid3d html
equidistantCurve html
exVar html
fastKmeans html
find.outliers html
fixLMmirror html
fixLMtps html
getFaces html
getMeaningfulPCs html
getOuterViewpoints html
finding level-2 HTML links ... done
getPCscores html
getPCtol html
getPLSCommonShape html
getPLSfromScores html
getPLSscores html
getPointAlongOutline html
getSides html
getTrafo4x4 html
getTrafoRotaxis html
getVisibleVertices html
groupPCA html
histGroup html
icpmat html
invertFaces html
kendalldist html
line2plane html
lineplot html
list2array html
mcNNindex html
mergeMeshes html
mesh2grey html
mesh2ply html
meshDist html
meshPlaneIntersect html
meshcube html
meshres html
mirror html
mirror2plane html
name2factor html
nose html
pcAlign html
pcaplot3d html
permudist html
permuvec html
placePatch html
plot.slider3d html
plotAtlas html
plotNormals html
pls2B html
plsCoVar html
plsCoVarCommonShape html
ply2mesh html
points2plane html
prcompfast html
predict.CVA html
predict.bgPCA html
predictPLSfromData html
predictPLSfromScores html
predictRelWarps html
predictShape.lm html
proc.weight html
procAOVsym html
procSym html
projRead html
qqmat html
quad2trimesh html
r2morphoj html
ray2mesh html
read.csv.folder html
read.fcsv html
read.lmdta html
read.mpp html
read.pts html
read.slicerjson html
readLandmarks.csv html
readallTPS html
regdist html
relWarps html
relaxLM html
render html
resampleCurve html
restoreFromPCA html
restoreShapes html
retroDeform3d html
retroDeformMesh html
rotaxis3d html
rotaxisMat html
rotmesh.onto html
rotonmat html
rotonto html
scalemesh html
slider2d html
slider3d html
solutionSpace html
sortCurve html
symmetrize html
tangentPlane html
tps3d html
typprob html
updateIndices html
updateNormals html
vecx html
vertex html
virtualMeshScan html
warpmovie3d html
write.fcsv html
write.pts html
write.slicerjson html
** 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 (Morpho)