##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:miloR.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings miloR_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/miloR.Rcheck'
* using R version 4.4.0 (2024-04-24 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'miloR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'miloR' version '2.0.0'
* 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 whether package 'miloR' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* checking installed package size ... OK
* 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/miloR/libs/x64/miloR.dll':
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
findNhoodMarkers 4.42   1.78    6.67
testNhoods       4.31   1.64    6.05
testDiffExp      5.58   0.12    5.70
checkSeparation  3.37   1.67    5.26
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/miloR.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL miloR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'miloR' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp: In function 'arma::mat initialiseG(Rcpp::List, arma::vec)':
computeMatrices.cpp:135:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
  135 |     for(unsigned long k=0; k < stot; k++){
      |                            ~~^~~~~~
computeMatrices.cpp:143:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  143 |             for(int l=0; l < q; l++){
      |                          ~~^~~
computeMatrices.cpp: In function 'arma::mat invGmat(Rcpp::List, arma::vec)':
computeMatrices.cpp:327:30: warning: comparison of integer expressions of different signedness: 'long unsigned int' and 'int' [-Wsign-compare]
  327 |     for(unsigned long k=0; k < stot; k++){
      |                            ~~^~~~~~
computeMatrices.cpp:335:28: warning: comparison of integer expressions of different signedness: 'int' and 'long unsigned int' [-Wsign-compare]
  335 |             for(int l=0; l < q; l++){
      |                          ~~^~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:197:10: warning: unused variable '_phi_est' [-Wunused-variable]
  197 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:177:10: warning: unused variable '_phi_est' [-Wunused-variable]
  177 |     bool _phi_est = true; // control if we re-estimate phi or not
      |          ^~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c inference.cpp -o inference.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c invertPseudoVar.cpp -o invertPseudoVar.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c multiP.cpp -o multiP.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c paramEst.cpp -o paramEst.o
paramEst.cpp:46: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   46 |     #pragma omp parallel for
      | 
paramEst.cpp:50: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   50 |         #pragma omp parallel for
      | 
paramEst.cpp:257: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  257 |     #pragma omp parallel for private(i, j, _ycovij)
      | 
paramEst.cpp:301: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  301 |     #pragma omp parallel for private(i, j, _ycovij)
      | 
paramEst.cpp:380: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  380 |     #pragma omp parallel for private(i, j, _ycovij)
      | 
paramEst.cpp:489: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  489 |     #pragma omp parallel for private(i, j, _ycovij)
      | 
paramEst.cpp:714: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  714 |             #pragma omp parallel for reduction(+:temp_value)
      | 
paramEst.cpp:729: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
  729 |             #pragma omp parallel for reduction(+:temp_value)
      | 
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&)':
paramEst.cpp:29:33: warning: left operand of comma operator has no effect [-Wunused-value]
   29 |         double rhs = 0.5 * mid1[0, 0];
      |                                 ^
paramEst.cpp: In function 'arma::vec estHasemanElstonGenetic(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&)':
paramEst.cpp:258:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  258 |     for (int i = 0; i < n; i++) {
      |                     ~~^~~
paramEst.cpp:259:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  259 |         for (int j = i; j < n; j++) {
      |                         ~~^~~
paramEst.cpp:252:18: warning: unused variable 'i' [-Wunused-variable]
  252 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:252:21: warning: unused variable 'j' [-Wunused-variable]
  252 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:253:12: warning: unused variable '_ycovij' [-Wunused-variable]
  253 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElston(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&)':
paramEst.cpp:302:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  302 |     for (int i = 0; i < n; i++) {
      |                     ~~^~~
paramEst.cpp:303:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  303 |         for (int j = i; j < n; j++) {
      |                         ~~^~~
paramEst.cpp:294:18: warning: unused variable 'i' [-Wunused-variable]
  294 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:294:21: warning: unused variable 'j' [-Wunused-variable]
  294 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:295:12: warning: unused variable '_ycovij' [-Wunused-variable]
  295 |     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&)':
paramEst.cpp:381:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  381 |     for (int i = 0; i < n; i++) {
      |                     ~~^~~
paramEst.cpp:382:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  382 |         for (int j = i; j < n; j++) {
      |                         ~~^~~
paramEst.cpp:373:18: warning: unused variable 'i' [-Wunused-variable]
  373 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:373:21: warning: unused variable 'j' [-Wunused-variable]
  373 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:374:12: warning: unused variable '_ycovij' [-Wunused-variable]
  374 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec estHasemanElstonConstrainedGenetic(const arma::mat&, const arma::mat&, const Rcpp::List&, const arma::vec&, const arma::mat&, arma::vec, const int&)':
paramEst.cpp:490:23: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  490 |     for (int i = 0; i < n; i++) {
      |                     ~~^~~
paramEst.cpp:491:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  491 |         for (int j = i; j < n; j++) {
      |                         ~~^~~
paramEst.cpp:484:18: warning: unused variable 'i' [-Wunused-variable]
  484 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:484:21: warning: unused variable 'j' [-Wunused-variable]
  484 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                     ^
paramEst.cpp:485:12: warning: unused variable '_ycovij' [-Wunused-variable]
  485 |     double _ycovij; // Declare temp_value
      |            ^~~~~~~
paramEst.cpp: In function 'arma::vec nnlsSolve(const arma::mat&, const arma::vec&, arma::vec, const int&)':
paramEst.cpp:549:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  549 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:559:20: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  559 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:587:24: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  587 |         for(int i=0; i < m; i++){
      |                      ~~^~~
paramEst.cpp:623:28: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  623 |             for(int i=0; i < m; i++){
      |                          ~~^~~
paramEst.cpp:543:18: warning: variable 'inner_count' set but not used [-Wunused-but-set-variable]
  543 |     unsigned int inner_count = 0;
      |                  ^~~~~~~~~~~
paramEst.cpp:544:18: warning: unused variable 'outer_count' [-Wunused-variable]
  544 |     unsigned int outer_count = 0;
      |                  ^~~~~~~~~~~
paramEst.cpp: In function 'arma::mat vectoriseZ(const arma::mat&, const Rcpp::List&, const arma::mat&)':
paramEst.cpp:688:9: warning: unused variable 'j' [-Wunused-variable]
  688 |     int j, k, l, a;
      |         ^
paramEst.cpp:688:12: warning: unused variable 'k' [-Wunused-variable]
  688 |     int j, k, l, a;
      |            ^
paramEst.cpp:688:15: warning: unused variable 'l' [-Wunused-variable]
  688 |     int j, k, l, a;
      |               ^
paramEst.cpp:688:18: warning: unused variable 'a' [-Wunused-variable]
  688 |     int j, k, l, a;
      |                  ^
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:866:12: warning: unused variable 'half_logli' [-Wunused-variable]
  866 |     double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
      |            ^~~~~~~~~~
paramEst.cpp:871:10: warning: unused variable 'comp_vals' [-Wunused-variable]
  871 |     bool comp_vals = false;
      |          ^~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pseudovarPartial.cpp -o pseudovarPartial.o
pseudovarPartial.cpp:60: warning: ignoring '#pragma omp parallel' [-Wunknown-pragmas]
   60 |             #pragma omp parallel for reduction(+:temp_value)
      | 
pseudovarPartial.cpp: In function 'Rcpp::List pseudovarPartial_P(Rcpp::List, const arma::mat&)':
pseudovarPartial.cpp:58:27: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   58 |         for (int j = 0; j < n; j++) {
      |                         ~~^~~
pseudovarPartial.cpp:61:31: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   61 |             for (int k = 0; k < n; k++) {
      |                             ~~^~~
pseudovarPartial.cpp:64:32: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   64 |                 for(int a=0; a < n; a++){
      |                              ~~^~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppArmadillo/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -std=c++11   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -s -static-libgcc -o miloR.dll tmp.def RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRlapack -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lRblas -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-miloR/00new/miloR/libs/x64
** 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
** 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 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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.
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> 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, 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

Attaching package: 'IRanges'

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

    windows

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 

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution

warning: solve(): system is singular; attempting approx solution
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 213 ]
> 
> proc.time()
   user  system elapsed 
 293.90   27.71  322.82