Multiple platform build/check report for BioC 3.21 - BUILD BIN results for epistasisGA on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences"	4748
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"	4459
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4350
kjohnson3	macOS 13.6.5 Ventura	arm64	R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences"	4108
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 epistasisGA on kjohnson3

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

Version: 1.9.0

Command: rm -rf epistasisGA.buildbin-libdir && mkdir epistasisGA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh epistasisGA_1.9.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R epistasisGA.buildbin-libdir

StartedAt: 2024-11-26 07:30:14 -0500 (Tue, 26 Nov 2024)

EndedAt: 2024-11-26 07:30:28 -0500 (Tue, 26 Nov 2024)

EllapsedTime: 14.3 seconds

RetCode: 0

Status: OK

PackageFile: epistasisGA_1.9.0.tgz

PackageFileSize: 2.406 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf epistasisGA.buildbin-libdir && mkdir epistasisGA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh epistasisGA_1.9.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R epistasisGA.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=epistasisGA.buildbin-libdir epistasisGA_1.9.0.tar.gz'
>>>>>>> 

* installing *source* package ‘epistasisGA’ ...
** 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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/bigmemory/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -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/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/bigmemory/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -DR_NO_REMAP -c epistasisGA.cpp -o epistasisGA.o
epistasisGA.cpp:391:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
      if ((x(this_row , this_col) == 1) & (y(this_row, this_col) == 1)){
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                        &&
epistasisGA.cpp:391:11: note: cast one or both operands to int to silence this warning
epistasisGA.cpp:1952:14: warning: use of bitwise '|' with boolean operands [-Wbitwise-instead-of-logical]
        if ( (mutated_snps.length() != unique(mutated_snps).length()) | (sum(in(mutated_snps, target_chrom)) > 0) ){
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                                                      ||
epistasisGA.cpp:1952:14: note: cast one or both operands to int to silence this warning
epistasisGA.cpp:2511:9: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
    if ((is_true(any(mom_snps_l))) & (is_true(any(child_snps_l)))){
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                   &&
epistasisGA.cpp:2511:9: note: cast one or both operands to int to silence this warning
epistasisGA.cpp:2736:11: warning: use of bitwise '&' with boolean operands [-Wbitwise-instead-of-logical]
      if (null_mean_vec_.isNotNull() & null_se_vec_.isNotNull()){
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
                                     &&
epistasisGA.cpp:2736:11: note: cast one or both operands to int to silence this warning
4 warnings generated.
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 epistasisGA.so RcppExports.o epistasisGA.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-3.21-bioc/meat/epistasisGA.buildbin-libdir/00LOCK-epistasisGA/00new/epistasisGA/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 (epistasisGA)


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

>>>>>>> Paths before fix:
epistasisGA.buildbin-libdir/epistasisGA/libs/epistasisGA.so:
	epistasisGA.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0)
	/Library/Frameworks/R.framework/Versions/4.5-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/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "epistasisGA.buildbin-libdir/epistasisGA/libs/epistasisGA.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "epistasisGA.buildbin-libdir/epistasisGA/libs/epistasisGA.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "epistasisGA.buildbin-libdir/epistasisGA/libs/epistasisGA.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "epistasisGA.buildbin-libdir/epistasisGA/libs/epistasisGA.so"
install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "epistasisGA.buildbin-libdir/epistasisGA/libs/epistasisGA.so"

>>>>>>> Paths after fix:
epistasisGA.buildbin-libdir/epistasisGA/libs/epistasisGA.so:
	epistasisGA.so (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.5.0, current version 4.5.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0)
	/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.0)
	/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)