Multiple platform build/check report for BioC 3.23 - BUILD BIN results for GRENITS on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.3 LTS)	x86_64	R Under development (unstable) (2026-03-05 r89546) -- "Unsuffered Consequences"	4719
kjohnson3	macOS 13.7.7 Ventura	arm64	R Under development (unstable) (2026-03-01 r89506) -- "Unsuffered Consequences"	2847
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*

BUILD BIN results for GRENITS on kjohnson3

To the developers/maintainers of the GRENITS package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GRENITS.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.

raw results

Summary

Package: GRENITS

Version: 1.63.0

Command: rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GRENITS_1.63.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GRENITS.buildbin-libdir

StartedAt: 2026-03-10 16:34:12 -0400 (Tue, 10 Mar 2026)

EndedAt: 2026-03-10 16:34:38 -0400 (Tue, 10 Mar 2026)

EllapsedTime: 26.7 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf GRENITS.buildbin-libdir && mkdir GRENITS.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh GRENITS_1.63.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R GRENITS.buildbin-libdir
###
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##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=GRENITS.buildbin-libdir GRENITS_1.63.0.tar.gz'
>>>>>>> 

* installing *source* package ‘GRENITS’ ...
** this is package ‘GRENITS’ version ‘1.63.0’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.3.9.4)’
using SDK: ‘MacOSX14.4.sdk’
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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:49:30: warning: unused variable 'numDiag' [-Wunused-variable]
  int           num_fixedON, numDiag, p_sqr, free_gammas;
                             ^
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;
                                      ^
2 warnings generated.
clang++ -arch arm64 -std=gnu++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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++20 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.6/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.6/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.
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
clang++ -arch arm64 -std=gnu++20 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -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-darwin20.0/14.2.0 -L/opt/gfortran/lib -lemutls_w -lheapt_w -lgfortran -lquadmath -F/Library/Frameworks/R.framework/.. -framework R
'LdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
'RcppLdFlags' has not been needed since 2013 (!!) and may get removed in 2027. Please update your 'Makevars'.
installing to /Users/biocbuild/bbs-3.23-bioc/meat/GRENITS.buildbin-libdir/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)


>>>>>>> 
>>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR GRENITS.buildbin-libdir/GRENITS/libs/GRENITS.so
>>>>>>> 

>>>>>>> Paths before fix:
GRENITS.buildbin-libdir/GRENITS/libs/GRENITS.so:
	GRENITS.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRlapack.dylib (compatibility version 4.6.0, current version 4.6.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/14.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.6/Resources/lib/libR.dylib (compatibility version 4.6.0, current version 4.6.0)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 1700.255.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1345.100.2)
	/System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate (compatibility version 1.0.0, current version 4.0.0)

>>>>>>> Fix with install_name_tool:
ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib not found!