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###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:miloR.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings miloR_2.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/miloR.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 ‘miloR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘miloR’ version ‘2.2.0’
* package encoding: UTF-8
* 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 ‘miloR’ 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/miloR.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking installed package size ... NOTE
  installed size is 23.9Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs  21.4Mb
* 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 ... OK
* 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 ... NOTE
Unexported object imported by a ':::' call: ‘S4Vectors:::disableValidity’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotDAbeeswarm: no visible binding for global variable ‘SpatialFDR’
plotDAbeeswarm: no visible binding for global variable ‘logFC’
plotDAbeeswarm: no visible binding for global variable ‘is_signif’
plotDAbeeswarm: no visible binding for global variable ‘Nhood’
plotDAbeeswarm: no visible binding for global variable ‘logFC_color’
plotNhoodCounts: no visible binding for global variable ‘cond’
plotNhoodCounts: no visible binding for global variable ‘values’
plotNhoodCounts: no visible binding for global variable ‘y’
plotNhoodExpressionDA: no visible binding for global variable ‘Nhood’
plotNhoodExpressionDA: no visible binding for global variable ‘logFC’
plotNhoodExpressionDA: no visible binding for global variable
  ‘SpatialFDR’
plotNhoodExpressionDA: no visible binding for global variable
  ‘logFC_rank’
plotNhoodExpressionDA: no visible binding for global variable ‘.’
plotNhoodExpressionDA: no visible binding for global variable
  ‘is_signif’
plotNhoodExpressionDA: no visible binding for global variable ‘feature’
plotNhoodExpressionDA: no visible binding for global variable
  ‘avg_expr’
plotNhoodExpressionDA: no visible binding for global variable ‘label’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘Nhood’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘NhoodGroup’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘logFC’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘feature’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘logFC_rank’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘avg_expr’
plotNhoodExpressionGroups: no visible binding for global variable ‘.’
plotNhoodExpressionGroups: no visible binding for global variable
  ‘label’
plotNhoodGraph: no visible binding for global variable ‘weight’
plotNhoodGraph: no visible binding for global variable ‘size’
plotNhoodGraphDA: no visible binding for global variable ‘layout’
plotNhoodGroups: no visible binding for global variable ‘layout’
plotNhoodMA: no visible binding for global variable ‘logCPM’
plotNhoodMA: no visible binding for global variable ‘logFC’
plotNhoodMA: no visible binding for global variable ‘Sig’
plotNhoodSizeHist: no visible binding for global variable ‘nh_size’
testNhoods: no visible global function definition for ‘type’
Undefined global functions or variables:
  . Nhood NhoodGroup Sig SpatialFDR avg_expr cond feature is_signif
  label layout logCPM logFC logFC_color logFC_rank nh_size size type
  values weight y
Consider adding
  importFrom("graphics", "layout")
to your NAMESPACE file.
* 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
findNhoodMarkers 5.475  0.032   5.429
plotNhoodCounts  5.275  0.148   5.343
* 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/miloR.Rcheck/00check.log’
for details.

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### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL miloR
###
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* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.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 RcppExports.cpp:5:
/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
      |        ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp: In function 'arma::mat initialiseG(Rcpp::List, arma::vec)':
computeMatrices.cpp:144:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
  144 |     for(unsigned long k=0; k < stot; k++){
      |                            ~~^~~~~~
computeMatrices.cpp:152:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  152 |             for(int l=0; l < q; l++){
      |                          ~~^~~
computeMatrices.cpp: In function 'arma::mat invGmat(Rcpp::List, arma::vec)':
computeMatrices.cpp:336:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
  336 |     for(unsigned long k=0; k < stot; k++){
      |                            ~~^~~~~~
computeMatrices.cpp:344:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  344 |             for(int l=0; l < q; l++){
      |                          ~~^~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp: In function 'Rcpp::List fitGeneticPLGlmm(const arma::mat&, const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)':
fitGeneticPLGlmm.cpp:113:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
  113 |     double _intercept = constval; // intercept for HE regression
      |            ^~~~~~~~~~
fitGeneticPLGlmm.cpp:200:10: warning: unused variable '_phi_est' [-Wunused-variable]
  200 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp: In function 'Rcpp::List fitPLGlmm(const arma::mat&, const arma::mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const arma::vec&, Rcpp::List, double, const Rcpp::List&, double, const bool&, const int&, std::string, std::string)':
fitPLGlmm.cpp:106:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
  106 |     double _intercept = constval; // intercept for HE regression?? need a better estimate.
      |            ^~~~~~~~~~
fitPLGlmm.cpp:172:10: warning: unused variable '_phi_est' [-Wunused-variable]
  172 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c inference.cpp -o inference.o
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c invertPseudoVar.cpp -o invertPseudoVar.o
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c multiP.cpp -o multiP.o
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c paramEst.cpp -o paramEst.o
paramEst.cpp: In function 'arma::vec sigmaScoreREML_arma(const Rcpp::List&, const arma::vec&, const arma::mat&, const arma::vec&, const arma::mat&, const arma::mat&, const Rcpp::List&)':
paramEst.cpp:36:33: warning: left operand of comma operator has no effect [-Wunused-value]
   36 |         double rhs = 0.5 * mid1[0, 0];
      |                                 ^
paramEst.cpp: In function 'arma::vec solveEquations(const int&, const int&, const arma::mat&, const arma::mat&, const arma::mat&, const arma::vec&, const arma::vec&, const arma::vec&)':
paramEst.cpp:172:12: warning: unused variable 'lambda' [-Wunused-variable]
  172 |     double lambda = 1e-1;
      |            ^~~~~~
paramEst.cpp:173:12: warning: unused variable 'lambda_step' [-Wunused-variable]
  173 |     double lambda_step = 10;
      |            ^~~~~~~~~~~
paramEst.cpp:174:12: warning: unused variable '_illcond_eps' [-Wunused-variable]
  174 |     double _illcond_eps = 1e-6;
      |            ^~~~~~~~~~~~
paramEst.cpp:175:12: warning: unused variable '_lcond_target' [-Wunused-variable]
  175 |     double _lcond_target = 1e-5;
      |            ^~~~~~~~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonGenetic(const arma::mat&, const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&)':
paramEst.cpp:241:19: warning: unused variable 'nsq' [-Wunused-variable]
  241 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix, no diag
      |                   ^~~
paramEst.cpp:242:18: warning: unused variable 'i' [-Wunused-variable]
  242 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:242:21: warning: unused variable 'j' [-Wunused-variable]
  242 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:243:12: warning: unused variable '_ycovij' [-Wunused-variable]
  243 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElston(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&)':
paramEst.cpp:276:19: warning: unused variable 'nsq' [-Wunused-variable]
  276 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:277:18: warning: unused variable 'i' [-Wunused-variable]
  277 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:277:21: warning: unused variable 'j' [-Wunused-variable]
  277 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:278:12: warning: unused variable '_ycovij' [-Wunused-variable]
  278 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrained(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, arma::vec, const int&, const arma::mat&)':
paramEst.cpp:342:19: warning: unused variable 'nsq' [-Wunused-variable]
  342 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrainedGenetic(const arma::mat&, const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&, arma::vec, const int&)':
paramEst.cpp:409:19: warning: unused variable 'nsq' [-Wunused-variable]
  409 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:410:18: warning: unused variable 'i' [-Wunused-variable]
  410 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:410:21: warning: unused variable 'j' [-Wunused-variable]
  410 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrainedGeneticML(const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&, arma::vec, const int&)':
paramEst.cpp:442:19: warning: unused variable 'nsq' [-Wunused-variable]
  442 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:443:18: warning: unused variable 'i' [-Wunused-variable]
  443 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:443:21: warning: unused variable 'j' [-Wunused-variable]
  443 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp: In function 'arma::vec nnlsSolve(const arma::mat&, const arma::vec&, arma::vec, const int&)':
paramEst.cpp:478:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  478 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:488:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  488 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:515:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  515 |         for(int i=0; i < m; i++){
      |                      ~~^~~
paramEst.cpp:549:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  549 |             for(int i=0; i < m; i++){
      |                          ~~^~~
paramEst.cpp: In function 'double phiLineSearch(double, double, double, const int&, const arma::vec&, const arma::mat&, double, const arma::vec&, const arma::vec&, const arma::vec&)':
paramEst.cpp:774:12: warning: unused variable 'half_logli' [-Wunused-variable]
  774 |     double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
      |            ^~~~~~~~~~
paramEst.cpp:779:10: warning: unused variable 'comp_vals' [-Wunused-variable]
  779 |     bool comp_vals = false;
      |          ^~~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c pseudovarPartial.cpp -o pseudovarPartial.o
pseudovarPartial.cpp: In function 'Rcpp::List computePZList(const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const std::string&)':
pseudovarPartial.cpp:51:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   51 |     for(int i=0; i < c; i++){
      |                  ~~^~~
pseudovarPartial.cpp: In function 'Rcpp::List computePZList_G(const Rcpp::List&, const arma::mat&, const arma::mat&, const arma::mat&, const std::string&, const arma::mat&)':
pseudovarPartial.cpp:73:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   73 |     for(int i=0; i < c; i++){
      |                  ~~^~~
pseudovarPartial.cpp:77:14: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   77 |         if(i == c - 1){
      |            ~~^~~~~~~~
pseudovarPartial.cpp: In function 'Rcpp::List pseudovarPartial_P(Rcpp::List, const arma::mat&)':
pseudovarPartial.cpp:108:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  108 |         for (int j = 0; j < n; j++) {
      |                         ~~^~~
pseudovarPartial.cpp:110:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  110 |             for (int k = 0; k < n; k++) {
      |                             ~~^~~
pseudovarPartial.cpp:113:32: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  113 |                 for(int a=0; a < n; a++){
      |                              ~~^~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c solveQP.cpp -o solveQP.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 /home/biocbuild/R/R-4.4.1/site-library/RcppML/include/RcppMLCommon.hpp:36,
                 from solveQP.cpp:2:
/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
      |        ^~~~~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -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/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.4.1/site-library/RcppML/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fPIC  -g -O2  -Wall  -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.4.1/lib -L/usr/local/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o solveQP.o utils.o -lopenblas -L/usr/lib/gcc/aarch64-linux-gnu/10.3.1 -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/site-library/00LOCK-miloR/00new/miloR/libs
** R
** data
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘graph’ in package ‘miloR’
** 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 (miloR)

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

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(miloR)
Loading required package: edgeR
Loading required package: limma
> require(mvtnorm)
Loading required package: mvtnorm
> require(scran)
Loading required package: scran
Loading required package: SingleCellExperiment
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse,
    colCounts, colCummaxs, colCummins, colCumprods, colCumsums,
    colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs,
    colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats,
    colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads,
    colWeightedMeans, colWeightedMedians, colWeightedSds,
    colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet,
    rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods,
    rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps,
    rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins,
    rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks,
    rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following object is masked from 'package:limma':

    plotMA

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, saveRDS, setdiff, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians


Attaching package: 'SingleCellExperiment'

The following object is masked from 'package:edgeR':

    cpm

Loading required package: scuttle
> require(scater)
Loading required package: scater
Loading required package: ggplot2

Attaching package: 'scater'

The following object is masked from 'package:limma':

    plotMDS

> require(MASS)
Loading required package: MASS
> 
> test_check("miloR")
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected

Layout:
2 patch areas, spanning 2 columns and 1 rows

    t l b r
1:  1 1 1 1
2:  1 2 1 2
A patchwork composed of 2 patches
- Autotagging is turned off
- Guides are collected

Layout:
2 patch areas, spanning 2 columns and 1 rows

    t l b r
1:  1 1 1 1
2:  1 2 1 2
Coefficients not estimable: ConditionA 
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 214 ]
> 
> proc.time()
   user  system elapsed 
368.839   3.858 348.507