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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:scDDboost.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings scDDboost_1.8.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/scDDboost.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDDboost/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDDboost’ version ‘1.8.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘scDDboost’ can be installed ... WARNING
Found the following significant warnings:
  /home/biocbuild/R/R-4.4.1/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]
  /home/biocbuild/R/R-4.4.1/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]
See ‘/home/biocbuild/bbs-3.20-bioc/meat/scDDboost.Rcheck/00install.out’ for details.
* used C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS.md’:
No news entries found.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                    user system elapsed
scDDboost-package 60.032  1.538  23.085
pdd               59.750  1.453  23.418
sim_dat           16.279  0.208   0.016
detK              13.330  0.861   6.281
calD              12.502  0.395   6.042
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/scDDboost.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL scDDboost
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘scDDboost’ ...
** using staged installation
** libs
using C compiler: ‘gcc (conda-forge gcc 14.2.0-1) 14.2.0’
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c DATA.cpp -o DATA.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25,
                 from DATA.h:9,
                 from DATA.cpp:9:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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
      |        ^~~~~~~~~~~~~~~~~~~~
DATA.cpp: In member function 'std::vector<Eigen::Matrix<double, -1, -1> > DATA::reorg(Eigen::MatrixXd&, const Eigen::VectorXi&)':
DATA.cpp:17:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   17 |         for(int j = 0; j < s.size(); ++j){
      |                        ~~^~~~~~~~~~
DATA.cpp: In member function 'std::vector<Eigen::Matrix<double, -1, -1> > DATA::reorgr(const Eigen::MatrixXd&, const Eigen::VectorXi&)':
DATA.cpp:32:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   32 |         for(int j = 0; j < s.size(); ++j){
      |                        ~~^~~~~~~~~~
DATA.cpp: In member function 'r_q DATA::cal_r(Eigen::MatrixXd&, const Eigen::VectorXi&, const Eigen::VectorXd&)':
DATA.cpp:48:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   48 |     for(int i = 0; i < G; i++){
      |                    ~~^~~
DATA.cpp:49:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   49 |         for(int j = 0; j < nc; j++){
      |                        ~~^~~~
DATA.cpp:58:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   58 |     for(int i = 0; i < G; i++)
      |                    ~~^~~
DATA.cpp:59:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   59 |         for(int j = 0; j < K; j++){
      |                        ~~^~~
DATA.cpp:65:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   65 |             for(int t = 0; t < s.size(); t++)
      |                            ~~^~~~~~~~~~
DATA.cpp:70:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
   70 |             for(int t = 0; t < s.size(); t++)
      |                            ~~^~~~~~~~~~
DATA.cpp:85:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   85 |     for(int i = 0; i < G; ++i){
      |                    ~~^~~
DATA.cpp: In member function 'Eigen::MatrixXd DATA::cal_hp()':
DATA.cpp:106:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  106 |     for(int j=0;j<K;++j){
      |                 ~^~
DATA.cpp:113:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  113 |     for(int i=0;i<G;++i){
      |                 ~^~
DATA.cpp:114:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  114 |         for(int j=0;j<K;++j){
      |                     ~^~
DATA.cpp: In constructor 'DATA::DATA(Eigen::MatrixXd&, const Eigen::VectorXi&, const Eigen::VectorXd&, const Eigen::MatrixXi&)':
DATA.cpp:157:18: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  157 |     for(int j=0;j<K;j++){
      |                 ~^~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c Header.cpp -o Header.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25,
                 from Header.h:19,
                 from Header.cpp:9:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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
      |        ^~~~~~~~~~~~~~~~~~~~
Header.cpp: In function 'std::vector<std::vector<int> > partition(const int&)':
Header.cpp:38:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   38 |         for(int j=0;j<L;++j){
      |                     ~^~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c derived.cpp -o derived.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from derived.h:14,
                 from derived.cpp:9:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25,
                 from DATA.h:9,
                 from derived.h:13:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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
      |        ^~~~~~~~~~~~~~~~~~~~
derived.cpp: In constructor 'DC::DC(Eigen::MatrixXd&, Eigen::VectorXi&, Eigen::VectorXd&, std::vector<int>&, Eigen::MatrixXi&)':
derived.cpp:31:26: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
   31 |         for(int j = 0; j < K; j++){
      |                        ~~^~~
derived.cpp: In member function 'void DC::go_drv(const Eigen::MatrixXd&, const Eigen::MatrixXd&, double&, Eigen::VectorXd&, double, double)':
derived.cpp:162:22: warning: comparison of integer expressions of different signedness: 'int' and 'size_t' {aka 'long unsigned int'} [-Wsign-compare]
  162 |     for(int i = 0; i < G; i++)
      |                    ~~^~~
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c main.cpp -o main.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from derived.h:14,
                 from main.cpp:21:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
In file included from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Core:214,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/Eigen/Dense:1,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigenForward.h:28,
                 from /home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include/RcppEigen.h:25,
                 from main.cpp:9:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.4.1/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-4.4.1/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-4.4.1/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-4.4.1/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
      |        ^~~~~~~~~~~~~~~~~~~~
main.cpp: In function 'SEXPREC* new_D(SEXP, SEXP, SEXP)':
main.cpp:217:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  217 |     for(int i=0;i<de_i.size();i++){
      |                 ~^~~~~~~~~~~~
main.cpp:228:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  228 |     for(int i=0;i<cd.size();i++){
      |                 ~^~~~~~~~~~
main.cpp:229:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  229 |         for(int j=i+1;j<cd.size();j++){
      |                       ~^~~~~~~~~~
main.cpp:231:26: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  231 |             for(int t=0;t<de_i.size();t++){
      |                         ~^~~~~~~~~~~~
main.cpp: In function 'SEXPREC* pat(SEXP)':
main.cpp:283:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<int> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
  283 |     for(int i=0;i<res.size();i++)
      |                 ~^~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -c scDDboost_init.c -o scDDboost_init.o
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o scDDboost.so DATA.o Header.o derived.o main.o scDDboost_init.o -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-scDDboost/00new/scDDboost/libs
** R
** data
** 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 (scDDboost)

R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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> library(testthat)
> library(scDDboost)
Loading required package: ggplot2
> 
> test_check("scDDboost")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> proc.time()
   user  system elapsed 
 35.640   1.299  27.631