Pedro Baldoni
| Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/epigraHMM |
| git_branch: RELEASE_3_17 |
| git_last_commit: 7a4ec94 |
| git_last_commit_date: 2023-10-04 18:42:56 -0400 (Wed, 04 Oct 2023) |
| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:01 -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 641/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| epigraHMM 1.8.3 (landing page) Pedro Baldoni
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | WARNINGS | OK | | |||||||
|
To the developers/maintainers of the epigraHMM 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: epigraHMM |
| Version: 1.8.3 |
| Command: rm -rf epigraHMM.buildbin-libdir && mkdir epigraHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh epigraHMM_1.8.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R epigraHMM.buildbin-libdir |
| StartedAt: 2023-10-19 13:06:12 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 13:11:47 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 335.0 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: epigraHMM_1.8.3.tgz |
| PackageFileSize: 2.039 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf epigraHMM.buildbin-libdir && mkdir epigraHMM.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh epigraHMM_1.8.3.tar.gz /Library/Frameworks/R.framework/Resources/bin/R epigraHMM.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=epigraHMM.buildbin-libdir epigraHMM_1.8.3.tar.gz' >>>>>>> * installing *source* package ‘epigraHMM’ ... ** using staged installation ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c aggregate.cpp -o aggregate.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c computeBIC.cpp -o computeBIC.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c computeQFunction.cpp -o computeQFunction.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c computeViterbiSequence.cpp -o computeViterbiSequence.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c consensusRejectionControlled.cpp -o consensusRejectionControlled.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c differentialRejectionControlled.cpp -o differentialRejectionControlled.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c expStep.cpp -o expStep.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c getMarginalProbability.cpp -o getMarginalProbability.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c innerMaxStepProb.cpp -o innerMaxStepProb.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c maxStepProb.cpp -o maxStepProb.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c rbinomVectorized.cpp -o rbinomVectorized.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c reweight.cpp -o reweight.o clang++ -arch arm64 -std=gnu++11 -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'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include -DARMA_USE_HDF5 -fPIC -falign-functions=64 -Wall -g -O2 -c simulateMarkovChain.cpp -o simulateMarkovChain.o clang++ -arch arm64 -std=gnu++11 -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 epigraHMM.so RcppExports.o aggregate.o computeBIC.o computeQFunction.o computeViterbiSequence.o consensusRejectionControlled.o differentialRejectionControlled.o expStep.o getMarginalProbability.o innerMaxStepProb.o maxStepProb.o rbinomVectorized.o reweight.o simulateMarkovChain.o /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib/libhdf5.a -L/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rhdf5lib/lib -lcrypto -lcurl -lsz -laec -lz -ldl -lm -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 /Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/epigraHMM.buildbin-libdir/00LOCK-epigraHMM/00new/epigraHMM/libs ** R ** data *** moving datasets to lazyload DB ** 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 (epigraHMM) >>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR epigraHMM.buildbin-libdir/epigraHMM/libs/epigraHMM.so >>>>>>> >>>>>>> Paths before fix: epigraHMM.buildbin-libdir/epigraHMM/libs/epigraHMM.so: epigraHMM.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1) /Library/Frameworks/R.framework/Versions/4.3-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/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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) >>>>>>> Fix with install_name_tool: install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgcc_s.1.1.dylib" "epigraHMM.buildbin-libdir/epigraHMM/libs/epigraHMM.so" install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "epigraHMM.buildbin-libdir/epigraHMM/libs/epigraHMM.so" install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "epigraHMM.buildbin-libdir/epigraHMM/libs/epigraHMM.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib" "epigraHMM.buildbin-libdir/epigraHMM/libs/epigraHMM.so" install_name_tool -change "/opt/gfortran/lib/gcc/aarch64-apple-darwin20.0/12.2.0/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib" "epigraHMM.buildbin-libdir/epigraHMM/libs/epigraHMM.so" >>>>>>> Paths after fix: epigraHMM.buildbin-libdir/epigraHMM/libs/epigraHMM.so: epigraHMM.so (compatibility version 0.0.0, current version 0.0.0) /usr/lib/libcurl.4.dylib (compatibility version 7.0.0, current version 9.0.0) /usr/lib/libz.1.dylib (compatibility version 1.0.0, current version 1.2.11) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib (compatibility version 4.3.0, current version 4.3.1) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.dylib (compatibility version 0.0.0, current version 0.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libgfortran.5.dylib (compatibility version 6.0.0, current version 6.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libquadmath.0.dylib (compatibility version 1.0.0, current version 1.0.0) /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libR.dylib (compatibility version 4.3.0, current version 4.3.1) /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)