##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf rhdf5filters.buildbin-libdir && mkdir rhdf5filters.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rhdf5filters_1.9.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rhdf5filters.buildbin-libdir
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rhdf5filters.buildbin-libdir rhdf5filters_1.9.0.tar.gz'
>>>>>>> 

* installing *source* package ‘rhdf5filters’ ...
** using staged installation
rm: src/bzip2/libH5Zbz2.so.dSYM: is a directory
configuring the BLOSC filter...
x86_CPU=false
checking for gcc... clang -arch arm64
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether clang -arch arm64 accepts -g... yes
checking for clang -arch arm64 option to accept ISO C89... none needed
checking whether C compiler accepts -msse2... yes
checking whether C compiler accepts -mavx2... yes
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
configure:    BZIP2_LIB=bzip2/libH5Zbz2.so
configure:    BLOSC_LIB=blosc/libH5Zblosc.so
configure:    LZF_LIB=lzf/libH5Zlzf.so
configure: creating ./config.status
config.status: creating src/blosc/lib/blosc-1.20.1/Makefile
config.status: creating src/blosc/Makefile
config.status: creating src/Makevars
** libs
make -C blosc
make -C lib/snappy-1.1.1
clang++ -arch arm64 -std=gnu++14 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -c snappy.cc
snappy.cc:567:13: warning: unused function 'ComputeTable' [-Wunused-function]
static void ComputeTable() {
            ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -c snappy-c.cc
clang++ -arch arm64 -std=gnu++14 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -c snappy-sinksource.cc
clang++ -arch arm64 -std=gnu++14 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -c snappy-stubs-internal.cc
make -C lib/lz4-1.9.2
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c lz4.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c lz4hc.c
make -C lib/zstd-1.4.5
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/debug.c -o common/debug.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/entropy_common.c -o common/entropy_common.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/error_private.c -o common/error_private.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/fse_decompress.c -o common/fse_decompress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I. -c common/pool.c -o common/pool.o -o common/pool.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/threading.c -o common/threading.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/xxhash.c -o common/xxhash.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c common/zstd_common.c -o common/zstd_common.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/fse_compress.c -o compress/fse_compress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/hist.c -o compress/hist.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/huf_compress.c -o compress/huf_compress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress.c -o compress/zstd_compress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_literals.c -o compress/zstd_compress_literals.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_sequences.c -o compress/zstd_compress_sequences.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_compress_superblock.c -o compress/zstd_compress_superblock.o
compress/zstd_compress_superblock.c:412:12: warning: variable 'litLengthSum' set but not used [-Wunused-but-set-variable]
    size_t litLengthSum = 0;
           ^
1 warning generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_double_fast.c -o compress/zstd_double_fast.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_fast.c -o compress/zstd_fast.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_lazy.c -o compress/zstd_lazy.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_ldm.c -o compress/zstd_ldm.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstd_opt.c -o compress/zstd_opt.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c compress/zstdmt_compress.c -o compress/zstdmt_compress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/huf_decompress.c -o decompress/huf_decompress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_ddict.c -o decompress/zstd_ddict.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress.c -o decompress/zstd_decompress.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I. -I./common -DXXH_NAMESPACE=ZSTD_ -c decompress/zstd_decompress_block.c -o decompress/zstd_decompress_block.o
make -C lib/blosc-1.20.1 all
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c bitshuffle-generic.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c shuffle-generic.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5     -c shuffle.c
shuffle.c:316:22: warning: unused variable 'cpu_features' [-Wunused-variable]
  blosc_cpu_features cpu_features = blosc_get_cpu_features();
                     ^
In file included from shuffle.c:12:
./shuffle-generic.h:32:13: warning: unused function 'shuffle_generic_inline' [-Wunused-function]
static void shuffle_generic_inline(const size_t type_size,
            ^
./shuffle-generic.h:61:13: warning: unused function 'unshuffle_generic_inline' [-Wunused-function]
static void unshuffle_generic_inline(const size_t type_size,
            ^
3 warnings generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c blosclz.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c blosc.c
blosc.c:737:11: warning: variable 'ctbytes' set but not used [-Wunused-but-set-variable]
  int32_t ctbytes = 0;           /* number of compressed bytes in block */
          ^
1 warning generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -I../lz4-1.9.2 -I../snappy-1.1.1 -I../zstd-1.4.5   -c fastcopy.c
fastcopy.c:63:30: warning: unused function 'copy_5_bytes' [-Wunused-function]
static inline unsigned char *copy_5_bytes(unsigned char *out, const unsigned char *from) {
                             ^
fastcopy.c:68:30: warning: unused function 'copy_6_bytes' [-Wunused-function]
static inline unsigned char *copy_6_bytes(unsigned char *out, const unsigned char *from) {
                             ^
fastcopy.c:73:30: warning: unused function 'copy_7_bytes' [-Wunused-function]
static inline unsigned char *copy_7_bytes(unsigned char *out, const unsigned char *from) {
                             ^
3 warnings generated.
rm -f libblosc.a
ar cq libblosc.a lib/blosc-1.20.1/blosc.o lib/blosc-1.20.1/bitshuffle-generic.o lib/blosc-1.20.1/blosclz.o lib/blosc-1.20.1/shuffle.o lib/blosc-1.20.1/fastcopy.o lib/blosc-1.20.1/shuffle-generic.o lib/snappy-1.1.1/snappy.o lib/snappy-1.1.1/snappy-c.o lib/snappy-1.1.1/snappy-sinksource.o lib/snappy-1.1.1/snappy-stubs-internal.o lib/lz4-1.9.2/lz4.o lib/lz4-1.9.2/lz4hc.o lib/zstd-1.4.5/common/debug.o lib/zstd-1.4.5/common/entropy_common.o lib/zstd-1.4.5/common/error_private.o lib/zstd-1.4.5/common/fse_decompress.o lib/zstd-1.4.5/common/pool.o lib/zstd-1.4.5/common/threading.o lib/zstd-1.4.5/common/xxhash.o lib/zstd-1.4.5/common/zstd_common.o lib/zstd-1.4.5/compress/fse_compress.o lib/zstd-1.4.5/compress/hist.o lib/zstd-1.4.5/compress/huf_compress.o lib/zstd-1.4.5/compress/zstd_compress.o lib/zstd-1.4.5/compress/zstd_compress_literals.o lib/zstd-1.4.5/compress/zstd_compress_sequences.o lib/zstd-1.4.5/compress/zstd_compress_superblock.o lib/zstd-1.4.5/compress/zstd_double_fast.o lib/zstd-1.4.5/compress/zstd_fast.o lib/zstd-1.4.5/compress/zstd_lazy.o lib/zstd-1.4.5/compress/zstd_ldm.o lib/zstd-1.4.5/compress/zstd_opt.o lib/zstd-1.4.5/compress/zstdmt_compress.o lib/zstd-1.4.5/decompress/huf_decompress.o lib/zstd-1.4.5/decompress/zstd_ddict.o lib/zstd-1.4.5/decompress/zstd_decompress.o lib/zstd-1.4.5/decompress/zstd_decompress_block.o
ranlib libblosc.a
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c -o H5Zblosc.o H5Zblosc.c \
	-I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -I./lib/blosc-1.20.1
H5Zblosc.c:96:10: warning: unused variable 'errmsg' [-Wunused-variable]
    char errmsg[256];
         ^
1 warning generated.
clang++ -arch arm64 -std=gnu++14 -falign-functions=64 -Wall -g -O2 -fPIC -L/opt/R/arm64/lib -shared -o libH5Zblosc.so H5Zblosc.o \
	libblosc.a -lz
make -C bzip2
make -C bzip2-1.0.8
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -c blocksort.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -c huffman.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -c crctable.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -c randtable.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -c compress.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -c decompress.c
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -D_FILE_OFFSET_BITS=64 -c bzlib.c
rm -f libbz2.a
ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o
ranlib libbz2.a
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -shared H5Zbzip2.c -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" \
	-I./bzip2-1.0.8/ ./bzip2-1.0.8/libbz2.a -L/opt/R/arm64/lib -o libH5Zbz2.so
make -C lzf
make -C lzf
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c lzf_c.c
In file included from lzf_c.c:37:
./lzfP.h:138:6: warning: macro expansion producing 'defined' has undefined behavior [-Wexpansion-to-defined]
#if !STRICT_ALIGN
     ^
./lzfP.h:82:25: note: expanded from macro 'STRICT_ALIGN'
# define STRICT_ALIGN !(defined(__i386) || defined (__amd64))
                        ^
./lzfP.h:138:6: warning: macro expansion producing 'defined' has undefined behavior [-Wexpansion-to-defined]
./lzfP.h:82:44: note: expanded from macro 'STRICT_ALIGN'
# define STRICT_ALIGN !(defined(__i386) || defined (__amd64))
                                           ^
lzf_c.c:154:5: warning: macro expansion producing 'defined' has undefined behavior [-Wexpansion-to-defined]
#if STRICT_ALIGN
    ^
./lzfP.h:82:25: note: expanded from macro 'STRICT_ALIGN'
# define STRICT_ALIGN !(defined(__i386) || defined (__amd64))
                        ^
lzf_c.c:154:5: warning: macro expansion producing 'defined' has undefined behavior [-Wexpansion-to-defined]
./lzfP.h:82:44: note: expanded from macro 'STRICT_ALIGN'
# define STRICT_ALIGN !(defined(__i386) || defined (__amd64))
                                           ^
4 warnings generated.
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -c lzf_d.c
In file included from lzf_d.c:37:
./lzfP.h:138:6: warning: macro expansion producing 'defined' has undefined behavior [-Wexpansion-to-defined]
#if !STRICT_ALIGN
     ^
./lzfP.h:82:25: note: expanded from macro 'STRICT_ALIGN'
# define STRICT_ALIGN !(defined(__i386) || defined (__amd64))
                        ^
./lzfP.h:138:6: warning: macro expansion producing 'defined' has undefined behavior [-Wexpansion-to-defined]
./lzfP.h:82:44: note: expanded from macro 'STRICT_ALIGN'
# define STRICT_ALIGN !(defined(__i386) || defined (__amd64))
                                           ^
2 warnings generated.
rm -f liblzf.a
ar cq liblzf.a lzf_c.o lzf_d.o
clang -arch arm64 -falign-functions=64 -Wall -g -O2 -fPIC -shared H5Zlzf.c -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" \
	-I./lzf/ ./lzf/liblzf.a -L/opt/R/arm64/lib -o libH5Zlzf.so
mkdir -p "/Users/biocbuild/bbs-3.16-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp bzip2/libH5Zbz2.so "/Users/biocbuild/bbs-3.16-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp blosc/libH5Zblosc.so "/Users/biocbuild/bbs-3.16-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
cp lzf/libH5Zlzf.so "/Users/biocbuild/bbs-3.16-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/lib/"
clang -arch arm64 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/opt/R/arm64/include -I"/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include" -I'/Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/library/Rhdf5lib/include' -I/opt/R/arm64/include  -falign-functions=64 -Wall -g -O2 -fPIC  -falign-functions=64 -Wall -g -O2  -c rhdf5filters.c -o rhdf5filters.o
clang -arch arm64 -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 rhdf5filters.so rhdf5filters.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.16-bioc/meat/rhdf5filters.buildbin-libdir/00LOCK-rhdf5filters/00new/rhdf5filters/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** 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 (rhdf5filters)


>>>>>>> 
>>>>>>> FIXING LINKS FOR rhdf5filters.buildbin-libdir/rhdf5filters/libs/rhdf5filters.so
>>>>>>> 

ERROR: R installation problem: File /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libgcc_s.1.dylib not found!