Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-11-09 21:30 -0500 (Sat, 09 Nov 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4505 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4506 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4538 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4486 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
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 665/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
epistasisGA 1.8.0 (landing page) Michael Nodzenski
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
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. |
Package: epistasisGA |
Version: 1.8.0 |
Command: rm -rf epistasisGA.buildbin-libdir && mkdir epistasisGA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh epistasisGA_1.8.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R epistasisGA.buildbin-libdir |
StartedAt: 2024-11-09 16:48:24 -0500 (Sat, 09 Nov 2024) |
EndedAt: 2024-11-09 16:48:38 -0500 (Sat, 09 Nov 2024) |
EllapsedTime: 14.2 seconds |
RetCode: 0 |
Status: OK |
PackageFile: epistasisGA_1.8.0.tgz |
PackageFileSize: 2.405 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf epistasisGA.buildbin-libdir && mkdir epistasisGA.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh epistasisGA_1.8.0.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_1.8.0.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/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/bigmemory/include' -I/opt/R/arm64/include -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'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/bigmemory/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -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-3.20-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/4.4-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" "epistasisGA.buildbin-libdir/epistasisGA/libs/epistasisGA.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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/4.4-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/4.4-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/4.4-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)