* installing to library '/home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages'
* installing *source* package 'nimble' ...
** package 'nimble' successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether clang++-14 -std=gnu++11 accepts -g... yes
working on eigen
checking how to run the C++ preprocessor... clang++-14 -std=gnu++11 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking Eigen/Dense usability... no
checking Eigen/Dense presence... no
checking for Eigen/Dense... no
Using the version of Eigen provided with NIMBLE
ENABLE_LIB=true
configure: creating ./config.status
config.status: creating inst/make/Makevars
config.status: creating inst/make/Makevars_lib
config.status: creating R/config.R
config.status: creating src/Makevars
removing debugging flags
make[1]: Entering directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/inst/CppCode'
/home/hornik/tmp/R.check/r-devel-clang/Work/build/bin/Rscript --vanilla ./customizeMakeconf.R
make[1]: Leaving directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/inst/CppCode'
Building libnimble
make[1]: Entering directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/inst/CppCode'
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c RcppUtils.cpp -o RcppUtils.o
RcppUtils.cpp:48:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if(!Rf_isArray(Sx) & !Rf_isMatrix(Sx)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
RcppUtils.cpp:48:6: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c EigenTypedefs.cpp -o EigenTypedefs.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c eigenUsingClasses.cpp -o eigenUsingClasses.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c RcppNimbleUtils.cpp -o RcppNimbleUtils.o
RcppNimbleUtils.cpp:298:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if(!R_ExternalPtrAddr(SextptrFrom) | !R_ExternalPtrAddr(SextptrFrom)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
RcppNimbleUtils.cpp:298:8: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c Utils.cpp -o Utils.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c NamedObjects.cpp -o NamedObjects.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c ModelClassUtils.cpp -o ModelClassUtils.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c accessorClasses.cpp -o accessorClasses.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c dists.cpp -o dists.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c nimDists.cpp -o nimDists.o
nimDists.cpp:159:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((x.dim()[1] != p) | (chol.dim()[0] != p) | (chol.dim()[1] != p)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:159:6: note: cast one or both operands to int to silence this warning
nimDists.cpp:159:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((x.dim()[1] != p) | (chol.dim()[0] != p) | (chol.dim()[1] != p)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:159:6: note: cast one or both operands to int to silence this warning
nimDists.cpp:189:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((ans.dim()[0] != p) | (ans.dim()[1] != p)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:189:8: note: cast one or both operands to int to silence this warning
nimDists.cpp:206:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((x.dim()[1] != p) | (chol.dim()[0] != p) | (chol.dim()[1] != p)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:206:6: note: cast one or both operands to int to silence this warning
nimDists.cpp:206:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((x.dim()[1] != p) | (chol.dim()[0] != p) | (chol.dim()[1] != p)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:206:6: note: cast one or both operands to int to silence this warning
nimDists.cpp:236:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((ans.dim()[0] != p) | (ans.dim()[1] != p)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:236:8: note: cast one or both operands to int to silence this warning
nimDists.cpp:263:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((chol.dim()[0] != n) | (chol.dim()[1] != n)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:263:6: note: cast one or both operands to int to silence this warning
nimDists.cpp:315:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((chol.dim()[0] != n) | (chol.dim()[1] != n)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:315:6: note: cast one or both operands to int to silence this warning
nimDists.cpp:361:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((x.dim()[0] != p) | (x.dim()[1] != p)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:361:6: note: cast one or both operands to int to silence this warning
nimDists.cpp:380:8: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((ans.dim()[0] != p) | (ans.dim()[1] != p)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimDists.cpp:380:8: note: cast one or both operands to int to silence this warning
10 warnings generated.
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c dllFinalizer.cpp -o dllFinalizer.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c nimbleGraph.cpp -o nimbleGraph.o
nimbleGraph.cpp:183:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((numEdges != edgesTo.size()) | (numEdges != edgesFrom2ParentExprIDs.size()) | (numNodes != types.size()) | (numNodes != names.size())) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimbleGraph.cpp:183:6: note: cast one or both operands to int to silence this warning
nimbleGraph.cpp:183:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((numEdges != edgesTo.size()) | (numEdges != edgesFrom2ParentExprIDs.size()) | (numNodes != types.size()) | (numNodes != names.size())) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimbleGraph.cpp:183:6: note: cast one or both operands to int to silence this warning
nimbleGraph.cpp:183:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((numEdges != edgesTo.size()) | (numEdges != edgesFrom2ParentExprIDs.size()) | (numNodes != types.size()) | (numNodes != names.size())) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimbleGraph.cpp:183:6: note: cast one or both operands to int to silence this warning
3 warnings generated.
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c smartPtrs.cpp -o smartPtrs.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c predefinedNimbleLists.cpp -o predefinedNimbleLists.o
clang++-14 -std=gnu++14 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I"../include" -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -O3 -Wall -pedantic -mtune=native -c nimOptim.cpp -o nimOptim.o
linking libnimble.so
Linux
clang++-14 -std=gnu++14 -shared -o libnimble.so RcppUtils.o EigenTypedefs.o eigenUsingClasses.o RcppNimbleUtils.o Utils.o NamedObjects.o ModelClassUtils.o accessorClasses.o dists.o nimDists.o dllFinalizer.o nimbleGraph.o smartPtrs.o predefinedNimbleLists.o nimOptim.o
rm *.o
make[1]: Leaving directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/inst/CppCode'
make[1]: Entering directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/inst/CppCode'
rm -f Makeconf
make[1]: Leaving directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/inst/CppCode'
** libs
make[1]: Entering directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/src'
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -g -O3 -Wall -pedantic -mtune=native -c RcppUtils.cpp -o RcppUtils.o
RcppUtils.cpp:48:6: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
if(!Rf_isArray(Sx) & !Rf_isMatrix(Sx)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
&&
RcppUtils.cpp:48:6: note: cast one or both operands to int to silence this warning
1 warning generated.
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -g -O3 -Wall -pedantic -mtune=native -c dists.cpp -o dists.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -g -O3 -Wall -pedantic -mtune=native -c eigenUsingClasses.cpp -o eigenUsingClasses.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -g -O3 -Wall -pedantic -mtune=native -c nimble.cpp -o nimble.o
clang++-14 -std=gnu++11 -I"/home/hornik/tmp/R.check/r-devel-clang/Work/build/include" -DNDEBUG -DR_NO_REMAP -I../inst/include -I/usr/local/include -D_FORTIFY_SOURCE=2 -fpic -g -O3 -Wall -pedantic -mtune=native -c nimbleGraph.cpp -o nimbleGraph.o
nimbleGraph.cpp:183:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((numEdges != edgesTo.size()) | (numEdges != edgesFrom2ParentExprIDs.size()) | (numNodes != types.size()) | (numNodes != names.size())) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimbleGraph.cpp:183:6: note: cast one or both operands to int to silence this warning
nimbleGraph.cpp:183:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((numEdges != edgesTo.size()) | (numEdges != edgesFrom2ParentExprIDs.size()) | (numNodes != types.size()) | (numNodes != names.size())) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimbleGraph.cpp:183:6: note: cast one or both operands to int to silence this warning
nimbleGraph.cpp:183:6: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
if((numEdges != edgesTo.size()) | (numEdges != edgesFrom2ParentExprIDs.size()) | (numNodes != types.size()) | (numNodes != names.size())) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
||
nimbleGraph.cpp:183:6: note: cast one or both operands to int to silence this warning
3 warnings generated.
clang++-14 -std=gnu++11 -shared -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -Wl,-O1 -o nimble.so RcppUtils.o dists.o eigenUsingClasses.o nimble.o nimbleGraph.o -llapack -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lRblas -L/usr/lib/gcc/x86_64-linux-gnu/11 -lgfortran -lm -lquadmath -L/home/hornik/tmp/R.check/r-devel-clang/Work/build/lib -lR
make[1]: Leaving directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/src'
make[1]: Entering directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/src'
make[1]: Leaving directory '/tmp/Rtmp51q10D/R.INSTALL2485b24a99624e/nimble/src'
installing to /home/hornik/tmp/R.check/r-devel-clang/Work/build/Packages/00LOCK-nimble/00new/nimble/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
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readelf: Warning: Bogus end-of-siblings marker detected at offset bf2a in .debug_info section
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readelf: Warning: Bogus end-of-siblings marker detected at offset c02a in .debug_info section
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readelf: Warning: DIE at offset 0xc059 refers to abbreviation number 935 which does not exist
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nimble)