Edward Morrissey
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/GRENITS |
| git_branch: RELEASE_3_17 |
| git_last_commit: 8a74e5e |
| git_last_commit_date: 2023-05-01 20:07:24 -0400 (Mon, 01 May 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:03 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 881/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| GRENITS 1.52.1 (landing page) Edward Morrissey
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK | | |||||||
|
To the developers/maintainers of the GRENITS 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: GRENITS |
| Version: 1.52.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRENITS |
| StartedAt: 2023-10-15 15:54:03 -0400 (Sun, 15 Oct 2023) |
| EndedAt: 2023-10-15 15:56:25 -0400 (Sun, 15 Oct 2023) |
| EllapsedTime: 142.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GRENITS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘GRENITS’ ...
** 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 arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AR1_Gauss_biocond.cc -o AR1_Gauss_biocond.o
AR1_Gauss_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable]
int num_fixedON, numDiag, p_sqr, free_gammas;
^
AR1_Gauss_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
int num_fixedON, numDiag, p_sqr, free_gammas;
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AR1_Student_biocond.cc -o AR1_Student_biocond.o
AR1_Student_biocond.cc:49:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
int num_fixedON, numDiag, p_sqr, free_gammas;
^
AR1_Student_biocond.cc:49:30: warning: unused variable 'numDiag' [-Wunused-variable]
int num_fixedON, numDiag, p_sqr, free_gammas;
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c AR1_biocond.cc -o AR1_biocond.o
AR1_biocond.cc:48:30: warning: unused variable 'numDiag' [-Wunused-variable]
int num_fixedON, numDiag, p_sqr, free_gammas;
^
AR1_biocond.cc:48:39: warning: variable 'p_sqr' set but not used [-Wunused-but-set-variable]
int num_fixedON, numDiag, p_sqr, free_gammas;
^
2 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c PSplines_biocond.cc -o PSplines_biocond.o
PSplines_biocond.cc:45:63: warning: unused variable 'numDiag' [-Wunused-variable]
int num_fixedON, nodesSpline, degreeSpline, numDiag, free_gammas;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_C_interface.cpp -o R_C_interface.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadMCMCFiles.cpp -o ReadMCMCFiles.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c commonFunctions.cc -o commonFunctions.o
commonFunctions.cc:315:36: warning: variable 'so_far_clock' set but not used [-Wunused-but-set-variable]
clock_t so_far_clock, time_now; //so_far_sec,
^
commonFunctions.cc:438:59: warning: unused variable 'num_on' [-Wunused-variable]
unsigned int num_on;
^
commonFunctions.cc:480:59: warning: unused variable 'num_on' [-Wunused-variable]
unsigned int num_on;
^
3 warnings generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c functionsErrorModel.cc -o functionsErrorModel.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c matrixManipulationFunctions.cc -o matrixManipulationFunctions.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c updateFunctions_AR1.cc -o updateFunctions_AR1.o
updateFunctions_AR1.cc:264:59: warning: unused variable 'num_on' [-Wunused-variable]
unsigned int num_on;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppArmadillo/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c updateFunctions_Splines.cc -o updateFunctions_Splines.o
updateFunctions_Splines.cc:158:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable]
int G, start_indx, end_indx;
^
updateFunctions_Splines.cc:158:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
int G, start_indx, end_indx;
^
updateFunctions_Splines.cc:182:16: warning: variable 'start_indx' set but not used [-Wunused-but-set-variable]
int G, start_indx, end_indx;
^
updateFunctions_Splines.cc:182:28: warning: variable 'end_indx' set but not used [-Wunused-but-set-variable]
int G, start_indx, end_indx;
^
4 warnings generated.
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o GRENITS.so AR1_Gauss_biocond.o AR1_Student_biocond.o AR1_biocond.o PSplines_biocond.o R_C_interface.o ReadMCMCFiles.o commonFunctions.o functionsErrorModel.o matrixManipulationFunctions.o updateFunctions_AR1.o updateFunctions_Splines.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
ld: warning: could not create compact unwind for ___emutls_get_address: registers 23 and 24 not saved contiguously in frame
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-GRENITS/00new/GRENITS/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** 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 (GRENITS)