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###
### Running command:
###
### rm -rf SeqArray.buildbin-libdir && mkdir SeqArray.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh SeqArray_1.38.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R SeqArray.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=SeqArray.buildbin-libdir SeqArray_1.38.0.tar.gz'
>>>>>>>
* installing *source* package ‘SeqArray’ ...
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvGDS2VCF.cpp -o ConvGDS2VCF.o
ConvGDS2VCF.cpp:182:12: 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]
pLine += sprintf(pLine, "%g", val);
^
/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 -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvToGDS.cpp -o ConvToGDS.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ConvVCF2GDS.cpp -o ConvVCF2GDS.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c FileMerge.cpp -o FileMerge.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c GetData.cpp -o GetData.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Index.cpp -o Index.o
Index.cpp:1109:4: 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(buffer, "%.0fs", s);
^
/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)))
^
Index.cpp:1111:4: 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(buffer, "%.1fm", s/S_MIN);
^
/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)))
^
Index.cpp:1113:4: 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(buffer, "%.1fh", s/S_HOUR);
^
/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)))
^
Index.cpp:1115:4: 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(buffer, "%.1fd", s/S_DAY);
^
/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)))
^
Index.cpp:1117:4: 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(buffer, "%.1f years", s/S_YEAR);
^
/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)))
^
Index.cpp:1309:12: 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]
int n = sprintf(buffer, "\r[%s] 100%%, completed, %s", bar, time_str(s));
^
/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)))
^
Index.cpp:1311:5: 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(buffer+n, " (process %d)", *R_Process_Index);
^
/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)))
^
Index.cpp:1317:12: 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]
int n = sprintf(buffer, "\r[%s] %2.0f%%, ETC: %s", bar, p, time_str(s));
^
/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)))
^
Index.cpp:1319:10: 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]
n += sprintf(buffer+n, " (process %d)", *R_Process_Index);
^
/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)))
^
9 warnings generated.
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c LinkSNPRelate.cpp -o LinkSNPRelate.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c Methods.cpp -o Methods.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c R_SeqArray.c -o R_SeqArray.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBySample.cpp -o ReadBySample.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadByUnit.cpp -o ReadByUnit.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c ReadByVariant.cpp -o ReadByVariant.o
clang++ -arch arm64 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c SeqArray.cpp -o SeqArray.o
SeqArray.cpp:1400:3: 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(buf_compiler, "GNUG_v%d.%d.%d", __GNUC__, __GNUC_MINOR__, __GNUC_PATCHLEVEL__);
^
/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 -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c pkg_test.cpp -o pkg_test.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c samtools_ext.c -o samtools_ext.o
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DUSING_R -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/gdsfmt/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c vectorization.c -o vectorization.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 SeqArray.so ConvGDS2VCF.o ConvToGDS.o ConvVCF2GDS.o FileMerge.o GetData.o Index.o LinkSNPRelate.o Methods.o R_SeqArray.o ReadBySample.o ReadByUnit.o ReadByVariant.o SeqArray.o pkg_test.o samtools_ext.o vectorization.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/SeqArray.buildbin-libdir/00LOCK-SeqArray/00new/SeqArray/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 (SeqArray)
>>>>>>>
>>>>>>> FIXING LINKS FOR SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.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" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.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" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.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" "SeqArray.buildbin-libdir/SeqArray/libs/SeqArray.so"
