Multiple platform build/check report for BioC 3.19 - INSTALL results for miloR on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*
INSTALL results for miloR on nebbiolo1

To the developers/maintainers of the miloR package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/miloR.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.
raw results
Summary

Package: miloR
Version: 2.0.0
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL miloR
StartedAt: 2024-10-16 16:39:55 -0400 (Wed, 16 Oct 2024)
EndedAt: 2024-10-16 16:41:40 -0400 (Wed, 16 Oct 2024)
EllapsedTime: 105.2 seconds
RetCode: 0
Status: OK
Command output

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### Running command:
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###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL miloR
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -std=gnu++11 -fopenmp -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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: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"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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 mat&, const mat&, const mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const vec&, Rcpp::List, double, const 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"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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 mat&, const mat&, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::vec, arma::mat, const vec&, Rcpp::List, double, const 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"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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 List&, const vec&, const mat&, const vec&, const mat&, const 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 mat&, const mat&, const List&, const vec&, const 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 mat&, const mat&, const List&, const 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 mat&, const mat&, const List&, const 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 mat&, const mat&, const List&, const vec&, const 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 mat&, const 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 mat&, const List&, const 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 vec&, const mat&, double, const vec&, const vec&, const 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;
      |          ^~~~~~~~~
paramEst.cpp: In function ‘arma::mat vectoriseZ(const mat&, const List&, const mat&)’:
paramEst.cpp:714:21: warning: ‘temp_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  714 |             #pragma omp parallel for reduction(+:temp_value)
      |                     ^~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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 pseudovarPartial_P(Rcpp::List, const 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++){
      |                              ~~^~~
pseudovarPartial.cpp:60:21: warning: ‘temp_value’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   60 |             #pragma omp parallel for reduction(+:temp_value)
      |                     ^~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.19-bioc/R/site-library/RcppArmadillo/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/bbs-3.19-bioc/R/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 utils.o -llapack -L/home/biocbuild/bbs-3.19-bioc/R/lib -lRblas -lgfortran -lm -lquadmath -fopenmp -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-bioc/R/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)