Mike Morgan
| Snapshot Date: 2025-10-24 13:45 -0400 (Fri, 24 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/miloR |
| git_branch: devel |
| git_last_commit: be20c8b |
| git_last_commit_date: 2025-08-29 09:57:51 -0400 (Fri, 29 Aug 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-25 12:07 -0400 (Sat, 25 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4901 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4691 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4637 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4658 |
| 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 1304/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 2.5.2 (landing page) Mike Morgan
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | NA | NA | ||||||||||
|
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: 2.5.2 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL miloR |
| StartedAt: 2025-10-23 21:17:46 -0000 (Thu, 23 Oct 2025) |
| EndedAt: 2025-10-23 21:21:18 -0000 (Thu, 23 Oct 2025) |
| EllapsedTime: 211.8 seconds |
| RetCode: 0 |
| Status: OK |
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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 ‘2.5.2’
** 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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from RcppExports.cpp:4:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:214,
from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigen.h:25,
from RcppExports.cpp:5:
/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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
| ^~~~~~~~~~~~~~~~~~~~
/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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c computeMatrices.cpp -o computeMatrices.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from computeMatrices.h:4,
from computeMatrices.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from fitGeneticPLGlmm.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c fitPLGlmm.cpp -o fitPLGlmm.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from fitPLGlmm.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c inference.cpp -o inference.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from inference.h:4,
from inference.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
/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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c invertPseudoVar.cpp -o invertPseudoVar.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from invertPseudoVar.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
/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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c multiP.cpp -o multiP.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from multiP.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
/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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c paramEst.cpp -o paramEst.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from paramEst.h:4,
from paramEst.cpp:2:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
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:37:33: warning: left operand of comma operator has no effect [-Wunused-value]
37 | 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:173:12: warning: unused variable ‘lambda’ [-Wunused-variable]
173 | double lambda = 1e-1;
| ^~~~~~
paramEst.cpp:174:12: warning: unused variable ‘lambda_step’ [-Wunused-variable]
174 | double lambda_step = 10;
| ^~~~~~~~~~~
paramEst.cpp:175:12: warning: unused variable ‘_illcond_eps’ [-Wunused-variable]
175 | double _illcond_eps = 1e-6;
| ^~~~~~~~~~~~
paramEst.cpp:176:12: warning: unused variable ‘_lcond_target’ [-Wunused-variable]
176 | 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:242:19: warning: unused variable ‘nsq’ [-Wunused-variable]
242 | unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix, no diag
| ^~~
paramEst.cpp:243:18: warning: unused variable ‘i’ [-Wunused-variable]
243 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:243:21: warning: unused variable ‘j’ [-Wunused-variable]
243 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:244:12: warning: unused variable ‘_ycovij’ [-Wunused-variable]
244 | 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:277:19: warning: unused variable ‘nsq’ [-Wunused-variable]
277 | unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
| ^~~
paramEst.cpp:278:18: warning: unused variable ‘i’ [-Wunused-variable]
278 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:278:21: warning: unused variable ‘j’ [-Wunused-variable]
278 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:279:12: warning: unused variable ‘_ycovij’ [-Wunused-variable]
279 | 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:343:19: warning: unused variable ‘nsq’ [-Wunused-variable]
343 | 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:410:19: warning: unused variable ‘nsq’ [-Wunused-variable]
410 | unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
| ^~~
paramEst.cpp:411:18: warning: unused variable ‘i’ [-Wunused-variable]
411 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:411:21: warning: unused variable ‘j’ [-Wunused-variable]
411 | 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:443:19: warning: unused variable ‘nsq’ [-Wunused-variable]
443 | unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
| ^~~
paramEst.cpp:444:18: warning: unused variable ‘i’ [-Wunused-variable]
444 | unsigned int i, j; // Declare loop variables i and j for OpenMP
| ^
paramEst.cpp:444:21: warning: unused variable ‘j’ [-Wunused-variable]
444 | 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:479:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
479 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:489:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
489 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:516:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
516 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:550:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
550 | 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:775:12: warning: unused variable ‘half_logli’ [-Wunused-variable]
775 | double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
| ^~~~~~~~~~
paramEst.cpp:780:10: warning: unused variable ‘comp_vals’ [-Wunused-variable]
780 | bool comp_vals = false;
| ^~~~~~~~~
/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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c pseudovarPartial.cpp -o pseudovarPartial.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from pseudovarPartial.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
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++){
| ~~^~~
/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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c solveQP.cpp -o solveQP.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from solveQP.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Core:214,
from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/Eigen/Dense:1,
from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigenForward.h:28,
from /home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include/RcppEigen.h:25,
from /home/biocbuild/R/R-4.5.0/site-library/RcppML/include/RcppMLCommon.hpp:36,
from solveQP.cpp:2:
/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/site-library/RcppEigen/include/Eigen/Core:172:
/home/biocbuild/R/R-4.5.0/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-4.5.0/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-4.5.0/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-4.5.0/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
| ^~~~~~~~~~~~~~~~~~~~
/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'/home/biocbuild/R/R-4.5.0/site-library/RcppEigen/include' -I'/home/biocbuild/R/R-4.5.0/site-library/RcppML/include' -I/usr/local/include -g -O2 -Wall -Werror=format-security -std=gnu++11 -fopenmp -fPIC -g -O2 -Wall -Werror=format-security -c utils.cpp -o utils.o
In file included from /home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo.h:29,
from utils.cpp:1:
/home/biocbuild/R/R-4.5.0/site-library/RcppArmadillo/include/RcppArmadillo/version/arma.h:66:199: note: ‘#pragma message: Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.’
66 | #pragma message("Using fallback compilation with Armadillo 14.6.3. Please consider defining -DARMA_USE_CURRENT and also removing C++11 compilation directive. See GitHub issue #475 for more.")
| ^
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/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 -lgfortran -lm -fopenmp -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/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)