Multiple platform build/check report for BioC 3.19 - BUILD BIN results for miloR on kjohnson1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 22.04.3 LTS)	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4763
palomino7	Windows Server 2022 Datacenter	x64	4.4.1 (2024-06-14 ucrt) -- "Race for Your Life"	4500
merida1	macOS 12.7.5 Monterey	x86_64	4.4.1 (2024-06-14) -- "Race for Your Life"	4530
kjohnson1	macOS 13.6.6 Ventura	arm64	4.4.1 (2024-06-14) -- "Race for Your Life"	4480
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 miloR on kjohnson1

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.

raw results

Summary

Package: miloR

Version: 2.0.0

Command: rm -rf miloR.buildbin-libdir && mkdir miloR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh miloR_2.0.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R miloR.buildbin-libdir

StartedAt: 2024-10-18 19:26:45 -0400 (Fri, 18 Oct 2024)

EndedAt: 2024-10-18 19:28:56 -0400 (Fri, 18 Oct 2024)

EllapsedTime: 131.7 seconds

RetCode: 0

Status: OK

PackageFile: miloR_2.0.0.tgz

PackageFileSize: 6.96 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf miloR.buildbin-libdir && mkdir miloR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh miloR_2.0.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R miloR.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=miloR.buildbin-libdir miloR_2.0.0.tar.gz'
>>>>>>> 

* installing *source* package ‘miloR’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
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 /Users/biocbuild/bbs-3.19-bioc/meat/miloR.buildbin-libdir/00LOCK-miloR/00new/miloR/libs
** R
** data
** inst
** 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)


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

>>>>>>> Paths before fix:
miloR.buildbin-libdir/miloR/libs/miloR.so:
	miloR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)

>>>>>>> Fix with install_name_tool:
install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgcc_s.1.1.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib" "miloR.buildbin-libdir/miloR/libs/miloR.so"

>>>>>>> Paths after fix:
miloR.buildbin-libdir/miloR/libs/miloR.so:
	miloR.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.4.0, current version 4.4.1)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libR.dylib (compatibility version 4.4.0, current version 4.4.1)
	/System/Library/Frameworks/CoreFoundation.framework/Versions/A/CoreFoundation (compatibility version 150.0.0, current version 1775.118.101)
	/usr/lib/libc++.1.dylib (compatibility version 1.0.0, current version 905.6.0)
	/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)