| Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2023-12-06 11:39:35 -0500 (Wed, 06 Dec 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4609 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2023-11-14 r85524 ucrt) -- "Unsuffered Consequences" | 4350 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2023-11-11 r85510) -- "Unsuffered Consequences" | 4375 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2023-11-01 r85459) -- "Unsuffered Consequences" | 4262 |
| 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 1234/2229 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 1.99.9 (landing page) Mike Morgan
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | TIMEOUT | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | TIMEOUT | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
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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: 1.99.9 |
| Command: /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL miloR |
| StartedAt: 2023-12-05 20:36:28 -0000 (Tue, 05 Dec 2023) |
| EndedAt: 2023-12-05 20:40:13 -0000 (Tue, 05 Dec 2023) |
| EllapsedTime: 224.4 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2023.11.02/bin/R CMD INSTALL miloR
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* installing to library ‘/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fPIC -g -O2 -Wall -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp: In function ‘arma::mat initialiseG(Rcpp::List, arma::vec)’:
computeMatrices.cpp:134:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
134 | for(unsigned long k=0; k < stot; k++){
| ~~^~~~~~
computeMatrices.cpp:142:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
142 | for(int l=0; l < q; l++){
| ~~^~~
computeMatrices.cpp: In function ‘arma::mat invGmat(Rcpp::List, arma::vec)’:
computeMatrices.cpp:326:30: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘int’ [-Wsign-compare]
326 | for(unsigned long k=0; k < stot; k++){
| ~~^~~~~~
computeMatrices.cpp:334:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘long unsigned int’ [-Wsign-compare]
334 | for(int l=0; l < q; l++){
| ~~^~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -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:198:10: warning: unused variable ‘_phi_est’ [-Wunused-variable]
198 | bool _phi_est = true; // control if we re-estimate phi or not
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -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:176:10: warning: unused variable ‘_phi_est’ [-Wunused-variable]
176 | bool _phi_est = true; // control if we re-estimate phi or not
| ^~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fPIC -g -O2 -Wall -c inference.cpp -o inference.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fPIC -g -O2 -Wall -c invertPseudoVar.cpp -o invertPseudoVar.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fPIC -g -O2 -Wall -c multiP.cpp -o multiP.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fPIC -g -O2 -Wall -c paramEst.cpp -o paramEst.o
paramEst.cpp: In function ‘arma::vec sigmaScoreREML_arma(const List&, const vec&, const mat&)’:
paramEst.cpp:24:33: warning: left operand of comma operator has no effect [-Wunused-value]
24 | double rhs = 0.5 * mid1[0, 0];
| ^
paramEst.cpp: In function ‘arma::vec nnlsSolve(const mat&, const vec&, arma::vec, const int&)’:
paramEst.cpp:639:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
639 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:649:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
649 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:677:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
677 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:713:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
713 | for(int i=0; i < m; i++){
| ~~^~~
paramEst.cpp:633:18: warning: variable ‘inner_count’ set but not used [-Wunused-but-set-variable]
633 | unsigned int inner_count = 0;
| ^~~~~~~~~~~
paramEst.cpp:634:18: warning: unused variable ‘outer_count’ [-Wunused-variable]
634 | unsigned int outer_count = 0;
| ^~~~~~~~~~~
paramEst.cpp: In function ‘double phiLineSearch(double, double, double, const int&, const vec&, const mat&, double, const vec&, const vec&, const vec&)’:
paramEst.cpp:924:12: warning: unused variable ‘half_logli’ [-Wunused-variable]
924 | double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
| ^~~~~~~~~~
paramEst.cpp:929:10: warning: unused variable ‘comp_vals’ [-Wunused-variable]
929 | bool comp_vals = false;
| ^~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fPIC -g -O2 -Wall -c pseudovarPartial.cpp -o pseudovarPartial.o
g++ -std=gnu++17 -I"/home/biocbuild/R/R-devel/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppArmadillo/include' -I'/home/biocbuild/R/R-4.4-devel-2023.11.02/site-library/RcppEigen/include' -I/usr/local/include -g -O2 -Wall -std=gnu++11 -fPIC -g -O2 -Wall -c utils.cpp -o utils.o
g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-devel/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 -lopenblas -lgfortran -lm -L/home/biocbuild/R/R-devel/lib -lR
installing to /home/biocbuild/R/R-4.4-devel-2023.11.02/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)