| Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-09-24 11:45 -0400 (Tue, 24 Sep 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4448 |
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4455 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4453 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4433 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4432 |
| 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 1249/2260 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 2.1.1 (landing page) Mike Morgan
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
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. |
| Package: miloR |
| Version: 2.1.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miloR |
| StartedAt: 2024-09-23 15:41:24 -0400 (Mon, 23 Sep 2024) |
| EndedAt: 2024-09-23 15:43:47 -0400 (Mon, 23 Sep 2024) |
| EllapsedTime: 142.8 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miloR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c computeMatrices.cpp -o computeMatrices.o
computeMatrices.cpp:246:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
int stot = 0;
^
1 warning generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c fitGeneticPLGlmm.cpp -o fitGeneticPLGlmm.o
fitGeneticPLGlmm.cpp:113:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
double _intercept = constval; // intercept for HE regression
^
fitGeneticPLGlmm.cpp:200:10: warning: unused variable '_phi_est' [-Wunused-variable]
bool _phi_est = true; // control if we re-estimate phi or not
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c fitPLGlmm.cpp -o fitPLGlmm.o
fitPLGlmm.cpp:172:10: warning: unused variable '_phi_est' [-Wunused-variable]
bool _phi_est = true; // control if we re-estimate phi or not
^
fitPLGlmm.cpp:106:12: warning: variable '_intercept' set but not used [-Wunused-but-set-variable]
double _intercept = constval; // intercept for HE regression?? need a better estimate.
^
2 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c inference.cpp -o inference.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c invertPseudoVar.cpp -o invertPseudoVar.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c multiP.cpp -o multiP.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c paramEst.cpp -o paramEst.o
paramEst.cpp:36:33: warning: left operand of comma operator has no effect [-Wunused-value]
double rhs = 0.5 * mid1[0, 0];
^
paramEst.cpp:172:12: warning: unused variable 'lambda' [-Wunused-variable]
double lambda = 1e-1;
^
paramEst.cpp:173:12: warning: unused variable 'lambda_step' [-Wunused-variable]
double lambda_step = 10;
^
paramEst.cpp:174:12: warning: unused variable '_illcond_eps' [-Wunused-variable]
double _illcond_eps = 1e-6;
^
paramEst.cpp:175:12: warning: unused variable '_lcond_target' [-Wunused-variable]
double _lcond_target = 1e-5;
^
paramEst.cpp:241:19: warning: unused variable 'nsq' [-Wunused-variable]
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]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:242:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:243:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:276:19: warning: unused variable 'nsq' [-Wunused-variable]
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]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:277:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:278:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:342:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:409:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:410:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:410:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:442:19: warning: unused variable 'nsq' [-Wunused-variable]
unsigned long nsq = (n * (n + 1)/2); //size of vectorised components using just upper or lower triangle of covariance matrix
^
paramEst.cpp:443:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:443:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:774:12: warning: unused variable 'half_logli' [-Wunused-variable]
double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
^
paramEst.cpp:779:10: warning: unused variable 'comp_vals' [-Wunused-variable]
bool comp_vals = false;
^
22 warnings generated.
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c pseudovarPartial.cpp -o pseudovarPartial.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c solveQP.cpp -o solveQP.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppEigen/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppML/include' -I/opt/R/x86_64/include -falign-functions=64 -Wall -g -O2 -std=gnu++11 -fPIC -falign-functions=64 -Wall -g -O2 -c utils.cpp -o utils.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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 -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/x86_64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/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)