Back to Mac ARM64 build report for BioC 3.16 |
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This page was generated on 2023-04-19 11:01:54 -0400 (Wed, 19 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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kjohnson | macOS 13.0 Ventura | arm64 | 4.2.2 (2022-10-31) -- "Innocent and Trusting" | 4256 |
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 |
To the developers/maintainers of the DeMixT package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 511/2183 | Hostname | OS / Arch | INSTALL | BUILD | BUILD BIN | ||||||||
DeMixT 1.14.0 (landing page) Shuai Guo
| kjohnson | macOS 13.0 Ventura / arm64 | OK | OK | OK | ||||||||
Package: DeMixT |
Version: 1.14.0 |
Command: rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DeMixT_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DeMixT.buildbin-libdir |
StartedAt: 2023-04-18 15:10:08 -0400 (Tue, 18 Apr 2023) |
EndedAt: 2023-04-18 15:12:39 -0400 (Tue, 18 Apr 2023) |
EllapsedTime: 150.8 seconds |
RetCode: 0 |
Status: OK |
PackageFile: DeMixT_1.14.0.tgz |
PackageFileSize: 2.684 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf DeMixT.buildbin-libdir && mkdir DeMixT.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh DeMixT_1.14.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R DeMixT.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=DeMixT.buildbin-libdir DeMixT_1.14.0.tar.gz' >>>>>>> * installing *source* package ‘DeMixT’ ... ** using staged installation ** libs clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c DeMixT.c -o DeMixT.o DeMixT.c:37:45: warning: variable 'st2_sig_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^ DeMixT.c:37:33: warning: variable 'st1_sig_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^ DeMixT.c:37:22: warning: variable 'st2_mu_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^ DeMixT.c:37:11: warning: variable 'st1_mu_2' set but not used [-Wunused-but-set-variable] double *st1_mu_2, *st2_mu_2, *st1_sig_2, *st2_sig_2; ^ DeMixT.c:591:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:591:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1280:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1280:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1307:18: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1307:9: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1322:21: warning: variable 'obj_new' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ DeMixT.c:1322:12: warning: variable 'obj_old' set but not used [-Wunused-but-set-variable] double obj_old, obj_new; ^ 12 warnings generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Profile_2D.cpp -o Profile_2D.o In file included from Profile_2D.cpp:5: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 1 warning generated. clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp.h:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/RcppCommon.h:168: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include/Rcpp/internal/r_coerce.h:255:7: warning: 'sprintf' is deprecated: This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead. [-Wdeprecated-declarations] ::sprintf(buff, "%02x", from); ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/stdio.h:188:1: note: 'sprintf' has been explicitly marked deprecated here __deprecated_msg("This function is provided for compatibility reasons only. Due to security concerns inherent in the design of sprintf(3), it is highly recommended that you use snprintf(3) instead.") ^ /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/sys/cdefs.h:215:48: note: expanded from macro '__deprecated_msg' #define __deprecated_msg(_msg) __attribute__((__deprecated__(_msg))) ^ 1 warning generated. clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c init.c -o init.o clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c registerDynamicSymbol.c -o registerDynamicSymbol.o clang++ -arch arm64 -std=gnu++14 -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 DeMixT.so DeMixT.o Profile_2D.o RcppExports.o init.o registerDynamicSymbol.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation ld: warning: -undefined dynamic_lookup may not work with chained fixups installing to /Volumes/External/bbs-3.16-bioc-m1/meat/DeMixT.buildbin-libdir/00LOCK-DeMixT/00new/DeMixT/libs ** R ** data *** moving datasets to lazyload DB ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location Warning: replacing previous import ‘ggplot2::alpha’ by ‘psych::alpha’ when loading ‘DeMixT’ Warning: replacing previous import ‘SummarizedExperiment::distance’ by ‘psych::distance’ when loading ‘DeMixT’ Warning: replacing previous import ‘ggplot2::%+%’ by ‘psych::%+%’ when loading ‘DeMixT’ ** testing if installed package keeps a record of temporary installation path * DONE (DeMixT) >>>>>>> >>>>>>> FIXING LINKS FOR DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so >>>>>>> install_name_tool -change "/opt/R/arm64/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgcc_s.1.1.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so" install_name_tool -change "/opt/R/arm64/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libgfortran.5.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so" install_name_tool -change "/opt/R/arm64/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libquadmath.0.dylib" "DeMixT.buildbin-libdir/DeMixT/libs/DeMixT.so"