##############################################################################
##############################################################################
###
### Running command:
###
### rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rhdf5_2.38.1.tar.gz /Library/Frameworks/R.framework/Resources/bin/R rhdf5.buildbin-libdir
###
##############################################################################
##############################################################################
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rhdf5.buildbin-libdir rhdf5_2.38.1.tar.gz'
>>>>>>>
* installing *source* package ‘rhdf5’ ...
** using staged installation
configure: creating ./config.status
config.status: creating src/external_filters.h
** libs
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5.c -o H5.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5A.c -o H5A.o
H5A.c:134:15: warning: variable 'Rval' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if ( ((b == 4) & (sgn == H5T_SGN_NONE)) | (b == 8) ) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5A.c:206:10: note: uninitialized use occurs here
return(Rval);
^~~~
H5A.c:134:10: note: remove the 'if' if its condition is always true
} else if ( ((b == 4) & (sgn == H5T_SGN_NONE)) | (b == 8) ) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5A.c:113:12: note: initialize the variable 'Rval' to silence this warning
SEXP Rval;
^
= NULL
H5A.c:245:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5D.c -o H5D.o
H5D.c:154:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:151:18: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_UCHAR);
^
H5D.c:183:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:180:18: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:216:24: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:213:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:265:24: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:262:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
^
H5D.c:251:20: warning: variable 'intbuf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:255:13: note: uninitialized use occurs here
if (intbuf == 0) {
^~~~~~
H5D.c:251:16: note: remove the 'if' if its condition is always true
} else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:241:21: note: initialize the variable 'intbuf' to silence this warning
void* intbuf;
^
= NULL
H5D.c:358:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:355:16: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
^
H5D.c:466:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tenum_insert (enumtype, st, &i);
^
H5D.c:476:24: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:473:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
^
H5D.c:554:24: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:551:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
^
H5D.c:570:24: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (superclass == H5T_FLOAT) {
^~~~~~~~~~~~~~~~~~~~~~~
H5D.c:576:98: note: uninitialized use occurs here
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^~~
H5D.c:570:20: note: remove the 'if' if its condition is always true
} else if (superclass == H5T_FLOAT) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:563:24: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (superclass == H5T_FLOAT) {
^~~~~~~~~~~~~~~~~~~~~~~
H5D.c:576:98: note: uninitialized use occurs here
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^~~
H5D.c:563:20: note: remove the 'if' if its condition is always true
} else if (superclass == H5T_FLOAT) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:558:19: note: initialize the variable 'buf' to silence this warning
void * buf;
^
= NULL
H5D.c:660:11: warning: unused variable 'mem_type_id' [-Wunused-variable]
hid_t mem_type_id = -1;
^
H5D.c:782:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tclose(dtype_id);
^
20 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5E.c -o H5E.o
H5E.c:66:5: warning: unused label 'Rf_error' [-Wunused-label]
error:
^~~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:52:15: note: expanded from macro 'error'
#define error Rf_error
^
H5E.c:75:15: warning: unused variable 'indent' [-Wunused-variable]
const int indent = 4;
^
H5E.c:98:5: warning: unused label 'Rf_error' [-Wunused-label]
error:
^~~~~~
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:52:15: note: expanded from macro 'error'
#define error Rf_error
^
H5E.c:110:16: warning: unused variable 'eee' [-Wunused-variable]
herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb, &client_data);
^
H5E.c:141:16: warning: unused variable 'eee' [-Wunused-variable]
herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data);
^
5 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5F.c -o H5F.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5G.c -o H5G.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5I.c -o H5I.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5L.c -o H5L.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5O.c -o H5O.o
H5O.c:13:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aiterate( obj_id, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &idx, &opAcount, &n);
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5P.c -o H5P.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5S.c -o H5S.o
H5S.c:258:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Sselect_hyperslab( space_id, op, start, stride, count, block );
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5S_extras.c -o H5S_extras.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5T.c -o H5T.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5Z.c -o H5Z.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5constants.c -o H5constants.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c HandleList.cpp -o HandleList.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c HandleListWrap.c -o HandleListWrap.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c bit64conversion.c -o bit64conversion.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c external_filters.c -o external_filters.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c h5dump.c -o h5dump.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c h5ls.c -o h5ls.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c h5testLock.c -o h5testLock.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c h5writeDataFrame.c -o h5writeDataFrame.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c printdatatype.c -o printdatatype.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c utils.c -o utils.o
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c wrap.c -o wrap.o
clang++ -mmacosx-version-min=10.13 -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/usr/local/lib -o rhdf5.so H5.o H5A.o H5D.o H5E.o H5F.o H5G.o H5I.o H5L.o H5O.o H5P.o H5S.o H5S_extras.o H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.14-bioc/meat/rhdf5.buildbin-libdir/00LOCK-rhdf5/00new/rhdf5/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 (rhdf5)
>>>>>>>
>>>>>>> FIXING LINKS FOR rhdf5.buildbin-libdir/rhdf5/libs/rhdf5.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgcc_s.1.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/rhdf5.so"
install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libgfortran.5.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/rhdf5.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libquadmath.0.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/rhdf5.so"
