Build/check report for BioC 3.24 - INSTALL results for miloR on nebbiolo2

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4800
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 nebbiolo2

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: 2.7.3
Command: /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL miloR
StartedAt: 2026-04-23 15:57:03 -0400 (Thu, 23 Apr 2026)
EndedAt: 2026-04-23 15:58:21 -0400 (Thu, 23 Apr 2026)
EllapsedTime: 78.1 seconds
RetCode: 1
Status: ERROR
Command output

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### Running command:
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###   /home/biocbuild/bbs-3.24-bioc/R/bin/R CMD INSTALL miloR
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* installing to library ‘/home/biocbuild/bbs-3.24-bioc/R/site-library’
* installing *source* package ‘miloR’ ...
** this is package ‘miloR’ version ‘2.7.3’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -Werror=format-security -fopenmp -g -O2  -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -Werror=format-security -fopenmp -g -O2  -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security  -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++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -Werror=format-security -fopenmp -g -O2  -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security  -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++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -Werror=format-security -fopenmp -g -O2  -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security  -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++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -Werror=format-security -fopenmp -g -O2  -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security  -c inference.cpp -o inference.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -Werror=format-security -fopenmp -g -O2  -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security  -c invertPseudoVar.cpp -o invertPseudoVar.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -Werror=format-security -fopenmp -g -O2  -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security  -c multiP.cpp -o multiP.o
g++ -std=gnu++20 -I"/home/biocbuild/bbs-3.24-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.24-bioc/R/site-library/RcppArmadillo/include' -I/usr/local/include   -g -O2  -Wall -Werror=format-security -fopenmp -g -O2  -Wall -Werror=format-security -fpic  -g -O2  -Wall -Werror=format-security  -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:36:34: warning: left operand of comma operator has no effect [-Wunused-value]
   36 |         double rhs = 0.5 * mid1[(0, 0]))
      |                                  ^
paramEst.cpp:36:38: error: expected ‘)’ before ‘]’ token
   36 |         double rhs = 0.5 * mid1[(0, 0]))
      |                                 ~    ^
      |                                      )
paramEst.cpp:38:34: error: expected ‘]’ before ‘;’ token
   38 |         reml_score[i] = lhs + rhs;
      |                                  ^
      |                                  ]
paramEst.cpp:33:16: warning: unused variable ‘lhs’ [-Wunused-variable]
   33 |         double lhs = -0.5 * arma::trace(Pdifi);
      |                ^~~
paramEst.cpp:36:16: warning: unused variable ‘rhs’ [-Wunused-variable]
   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:407:19: warning: unused variable ‘nsq’ [-Wunused-variable]
  407 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:408:18: warning: unused variable ‘i’ [-Wunused-variable]
  408 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:408:21: warning: unused variable ‘j’ [-Wunused-variable]
  408 |     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:439:19: warning: unused variable ‘nsq’ [-Wunused-variable]
  439 |     unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
      |                   ^~~
paramEst.cpp:440:18: warning: unused variable ‘i’ [-Wunused-variable]
  440 |     unsigned int i, j;      // Declare loop variables i and j for OpenMP
      |                  ^
paramEst.cpp:440:21: warning: unused variable ‘j’ [-Wunused-variable]
  440 |     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:474:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  474 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:484:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  484 |     for(int i=0; i < m; i++){
      |                  ~~^~~
paramEst.cpp:511:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  511 |         for(int i=0; i < m; i++){
      |                      ~~^~~
paramEst.cpp:545:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
  545 |             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:780:12: warning: unused variable ‘half_logli’ [-Wunused-variable]
  780 |     double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
      |            ^~~~~~~~~~
paramEst.cpp:785:10: warning: unused variable ‘comp_vals’ [-Wunused-variable]
  785 |     bool comp_vals = false;
      |          ^~~~~~~~~
make: *** [/home/biocbuild/bbs-3.24-bioc/R/etc/Makeconf:197: paramEst.o] Error 1
ERROR: compilation failed for package ‘miloR’
* removing ‘/home/biocbuild/bbs-3.24-bioc/R/site-library/miloR’
* restoring previous ‘/home/biocbuild/bbs-3.24-bioc/R/site-library/miloR’