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### Running command:
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###   /home/biocbuild/R/R/bin/R CMD INSTALL SPOTlight
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘SPOTlight’ ...
** this is package ‘SPOTlight’ version ‘1.12.1’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigen.h:25,
                 from RcppExports.cpp:4:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG  -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Rcpp/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include' -I/usr/local/include   -fopenmp -DEIGEN_INITIALIZE_MATRICES_BY_ZERO -DEIGEN_NO_DEBUG -fPIC  -g -O2  -Wall -Werror=format-security  -c nmf.cpp -o nmf.o
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/RcppEigen.h:25,
                 from nmf.cpp:17:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::pload(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1671:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1671 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h: In function ‘Packet Eigen::internal::ploadu(const typename unpacket_traits<T>::type*) [with Packet = eigen_packet_wrapper<int, 2>; typename unpacket_traits<T>::type = signed char]’:
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/arch/NEON/PacketMath.h:1716:9: warning: ‘void* memcpy(void*, const void*, size_t)’ copying an object of non-trivial type ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} from an array of ‘const int8_t’ {aka ‘const signed char’} [-Wclass-memaccess]
 1716 |   memcpy(&res, from, sizeof(Packet4c));
      |   ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/biocbuild/R/R-devel_2025-02-19/site-library/RcppEigen/include/Eigen/src/Core/GenericPacketMath.h:159:8: note: ‘Eigen::internal::Packet4c’ {aka ‘struct Eigen::internal::eigen_packet_wrapper<int, 2>’} declared here
  159 | struct eigen_packet_wrapper
      |        ^~~~~~~~~~~~~~~~~~~~
nmf.cpp: In function ‘void scale(Eigen::MatrixXd&, Eigen::VectorXd&)’:
nmf.cpp:95:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   95 |     for (size_t i = 0; i < w.rows(); ++i)
      |                        ~~^~~~~~~~~~
nmf.cpp:96:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
   96 |         for (size_t j = 0; j < w.cols(); ++j)
      |                            ~~^~~~~~~~~~
nmf.cpp: In function ‘void nnls(Eigen::MatrixXd&, Eigen::VectorXd&, Eigen::MatrixXd&, size_t)’:
nmf.cpp:130:30: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  130 |         for (size_t i = 0; i < h.rows(); ++i) {
      |                            ~~^~~~~~~~~~
nmf.cpp: In function ‘void c_predict(spmat, const Eigen::MatrixXd&, Eigen::MatrixXd&, double, double, int)’:
nmf.cpp:154:26: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘Eigen::Index’ {aka ‘long int’} [-Wsign-compare]
  154 |     for (size_t i = 0; i < h.cols(); ++i) {
      |                        ~~^~~~~~~~~~
nmf.cpp: In function ‘Eigen::MatrixXd predict_nmf(Rcpp::S4&, Eigen::MatrixXd&, double, double, int)’:
nmf.cpp:168:18: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  168 |     if (w.rows() == A.rows() && w.cols() != A.rows())
      |         ~~~~~~~~~^~~~~~~~~~~
nmf.cpp:168:42: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  168 |     if (w.rows() == A.rows() && w.cols() != A.rows())
      |                                 ~~~~~~~~~^~~~~~~~~~~
nmf.cpp: In function ‘Rcpp::List run_nmf(const Rcpp::S4&, const Rcpp::S4&, double, uint16_t, bool, double, double, uint16_t, Eigen::MatrixXd)’:
nmf.cpp:188:18: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  188 |     if (w.rows() == A.rows())
      |         ~~~~~~~~~^~~~~~~~~~~
nmf.cpp:190:23: warning: comparison of integer expressions of different signedness: ‘Eigen::Index’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  190 |     else if (w.cols() != A.rows())
      |              ~~~~~~~~~^~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o SPOTlight.so RcppExports.o nmf.o -fopenmp -L/home/biocbuild/R/R/lib -lRlapack -L/home/biocbuild/R/R/lib -lRblas -lgfortran -lm -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-SPOTlight/00new/SPOTlight/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (SPOTlight)