Mike Morgan
| Snapshot Date: 2024-05-06 14:00:02 -0400 (Mon, 06 May 2024) |
| git_url: https://git.bioconductor.org/packages/miloR |
| git_branch: RELEASE_3_19 |
| git_last_commit: 97eb8a7 |
| git_last_commit_date: 2024-04-30 11:34:02 -0400 (Tue, 30 Apr 2024) |
| Back to Mac ARM64 build report for BioC 3.19 |
|
This page was generated on 2024-05-07 11:32:38 -0400 (Tue, 07 May 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4461 |
| 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 1271/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| miloR 2.0.0 (landing page) Mike Morgan
| kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the miloR package: - 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: 2.0.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL miloR |
| StartedAt: 2024-05-06 15:53:36 -0400 (Mon, 06 May 2024) |
| EndedAt: 2024-05-06 15:54:08 -0400 (Mon, 06 May 2024) |
| EllapsedTime: 32.4 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-arm64/Resources/library’
* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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:237:9: warning: variable 'stot' set but not used [-Wunused-but-set-variable]
int stot = 0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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:197:10: warning: unused variable '_phi_est' [-Wunused-variable]
bool _phi_est = true; // control if we re-estimate phi or not
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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:177:10: warning: unused variable '_phi_est' [-Wunused-variable]
bool _phi_est = true; // control if we re-estimate phi or not
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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:29:33: warning: left operand of comma operator has no effect [-Wunused-value]
double rhs = 0.5 * mid1[0, 0];
^
paramEst.cpp:252:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:252:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:253:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:294:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:294:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:295:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:373:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:373:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:374:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:484:18: warning: unused variable 'i' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:484:21: warning: unused variable 'j' [-Wunused-variable]
unsigned int i, j; // Declare loop variables i and j for OpenMP
^
paramEst.cpp:485:12: warning: unused variable '_ycovij' [-Wunused-variable]
double _ycovij; // Declare temp_value
^
paramEst.cpp:543:18: warning: variable 'inner_count' set but not used [-Wunused-but-set-variable]
unsigned int inner_count = 0;
^
paramEst.cpp:544:18: warning: unused variable 'outer_count' [-Wunused-variable]
unsigned int outer_count = 0;
^
paramEst.cpp:688:9: warning: unused variable 'j' [-Wunused-variable]
int j, k, l, a;
^
paramEst.cpp:688:12: warning: unused variable 'k' [-Wunused-variable]
int j, k, l, a;
^
paramEst.cpp:688:15: warning: unused variable 'l' [-Wunused-variable]
int j, k, l, a;
^
paramEst.cpp:688:18: warning: unused variable 'a' [-Wunused-variable]
int j, k, l, a;
^
paramEst.cpp:866:12: warning: unused variable 'half_logli' [-Wunused-variable]
double half_logli = nbLogLik(mu, disp/2.0, y) - normlihood;
^
paramEst.cpp:871:10: warning: unused variable 'comp_vals' [-Wunused-variable]
bool comp_vals = false;
^
21 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/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 arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o miloR.so RcppExports.o computeMatrices.o fitGeneticPLGlmm.o fitPLGlmm.o inference.o invertPseudoVar.o multiP.o paramEst.o pseudovarPartial.o utils.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0 -L/opt/gfortran/lib -lgfortran -lemutls_w -lquadmath -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/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)