Back to Mac ARM64 build report for BioC 3.16 |
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This page was generated on 2023-04-19 11:01:53 -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 ChemmineR package: Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 304/2183 | Hostname | OS / Arch | INSTALL | BUILD | BUILD BIN | ||||||||
ChemmineR 3.50.0 (landing page) Thomas Girke
| kjohnson | macOS 13.0 Ventura / arm64 | OK | OK | OK | ||||||||
Package: ChemmineR |
Version: 3.50.0 |
Command: rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_3.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ChemmineR.buildbin-libdir |
StartedAt: 2023-04-18 14:22:26 -0400 (Tue, 18 Apr 2023) |
EndedAt: 2023-04-18 14:23:37 -0400 (Tue, 18 Apr 2023) |
EllapsedTime: 70.8 seconds |
RetCode: 0 |
Status: OK |
PackageFile: ChemmineR_3.50.0.tgz |
PackageFileSize: 2.286 MiB |
############################################################################## ############################################################################## ### ### Running command: ### ### rm -rf ChemmineR.buildbin-libdir && mkdir ChemmineR.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh ChemmineR_3.50.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R ChemmineR.buildbin-libdir ### ############################################################################## ############################################################################## >>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=ChemmineR.buildbin-libdir ChemmineR_3.50.0.tar.gz' >>>>>>> * installing *source* package ‘ChemmineR’ ... ** using staged installation ** libs 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c DisjointSets.cpp -o DisjointSets.o 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c cluster.cc -o cluster.o cluster.cc:49:13: warning: unused function 'prepare_neighbors' [-Wunused-function] void static prepare_neighbors(const char* nbr_file, int skip, int p) ^ 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c cstrsplit.cc -o cstrsplit.o In file included from cstrsplit.cc:2: 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))) ^ In file included from cstrsplit.cc:7: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:75:14: 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] std::sprintf( buffer, ":%ld", static_cast<long>( line() ) ); ^ /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))) ^ In file included from cstrsplit.cc:7: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string.hpp:23: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/split.hpp:16: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/iter_find.hpp:27: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/find_iterator.hpp:24: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/algorithm/string/detail/find_iterator.hpp:18: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function.hpp:30: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/function/detail/prologue.hpp:15: In file included from /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/throw_exception.hpp:24: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include/boost/assert/source_location.hpp:80:18: 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] std::sprintf( buffer, ":%ld", static_cast<long>( column() ) ); ^ /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))) ^ 3 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c desc.cc -o desc.o 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c fingerprints.cc -o fingerprints.o In file included from fingerprints.cc:12: 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c formats.cc -o formats.o 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c molecule.cc -o molecule.o 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c r_wrap.cc -o r_wrap.o r_wrap.cc:563:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register size_t l = 0; ^~~~~~~~~ r_wrap.cc:564:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register size_t r = iter->size - 1; ^~~~~~~~~ r_wrap.cc:567:2: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register size_t i = (l + r) >> 1; ^~~~~~~~~ r_wrap.cc:570:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register int compare = strcmp(name, iname); ^~~~~~~~~ r_wrap.cc:614:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register size_t i = 0; ^~~~~~~~~ r_wrap.cc:633:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register const unsigned char *u = (unsigned char *) ptr; ^~~~~~~~~ r_wrap.cc:634:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register const unsigned char *eu = u + sz; ^~~~~~~~~ r_wrap.cc:636:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register unsigned char uu = *u; ^~~~~~~~~ r_wrap.cc:648:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register unsigned char *u = (unsigned char *) ptr; ^~~~~~~~~ r_wrap.cc:649:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register const unsigned char *eu = u + sz; ^~~~~~~~~ r_wrap.cc:651:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register char d = *(c++); ^~~~~~~~~ r_wrap.cc:652:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register] register unsigned char uu; ^~~~~~~~~ r_wrap.cc:949:15: warning: variable 'p' set but not used [-Wunused-but-set-variable] const char *p = typeName; ^ r_wrap.cc:1689:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign] clientdata = clientdata; ~~~~~~~~~~ ^ ~~~~~~~~~~ 14 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c script.cc -o script.o 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'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/BH/include' -I/opt/R/arm64/include -DNO_MAIN -DNO_DEBUG -fPIC -falign-functions=64 -Wall -g -O2 -c similarity.cc -o similarity.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 ChemmineR.so DisjointSets.o cluster.o cstrsplit.o desc.o fingerprints.o formats.o molecule.o r_wrap.o script.o similarity.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/ChemmineR.buildbin-libdir/00LOCK-ChemmineR/00new/ChemmineR/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 (ChemmineR) >>>>>>> >>>>>>> FIXING LINKS FOR ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.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" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.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" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.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" "ChemmineR.buildbin-libdir/ChemmineR/libs/ChemmineR.so"