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This page was generated on 2026-05-06 11:34 -0400 (Wed, 06 May 2026).
| 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" | 4878 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4663 |
| 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 | ||||
| Package 1308/2366 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 2.9.1 (landing page) Mike Morgan
| nebbiolo2 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | ERROR | ERROR | skipped | |||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | ERROR | ERROR | skipped | ||||||||||
| See other builds for miloR in R Universe. | ||||||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: miloR |
| Version: 2.9.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL miloR |
| StartedAt: 2026-05-05 00:21:22 -0000 (Tue, 05 May 2026) |
| EndedAt: 2026-05-05 00:23:06 -0000 (Tue, 05 May 2026) |
| EllapsedTime: 104.2 seconds |
| RetCode: 1 |
| Status: ERROR |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL miloR
###
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* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘miloR’ ...
** this is package ‘miloR’ version ‘2.9.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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++){
| ~~^~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.5.0/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:36:40: error: expected ‘,’ or ‘;’ before ‘)’ token
36 | double rhs = 0.5 * mid1[(0, 0)])
| ^
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/R/R-4.5.0/etc/Makeconf:211: paramEst.o] Error 1
ERROR: compilation failed for package ‘miloR’
* removing ‘/home/biocbuild/R/R-4.5.0/site-library/miloR’
* restoring previous ‘/home/biocbuild/R/R-4.5.0/site-library/miloR’