##############################################################################
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###
### Running command:
###
### rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rhdf5_2.34.0.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rhdf5.buildbin-libdir
###
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rhdf5.buildbin-libdir rhdf5_2.34.0.tar.gz'
>>>>>>>
* installing *source* package ‘rhdf5’ ...
** using staged installation
Warning messages:
1: In readRDS(file) :
strings not representable in native encoding will be translated to UTF-8
2: In readRDS(file) :
strings not representable in native encoding will be translated to UTF-8
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/4.0/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/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5A.c -o H5A.o
H5A.c:142:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, buf );
^
H5A.c:175:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, buf );
^
H5A.c:202:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
H5A.c:209:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
4 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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:166:16: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^
H5D.c:179:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:176:18: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:190:16: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^
H5D.c:208:24: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:205:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:220:16: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^
H5D.c:254:24: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:251:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
^
H5D.c:259:16: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, intbuf );
^
H5D.c:240:20: warning: variable 'intbuf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:244:13: note: uninitialized use occurs here
if (intbuf == 0) {
^~~~~~
H5D.c:240:16: note: remove the 'if' if its condition is always true
} else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:230:21: note: initialize the variable 'intbuf' to silence this warning
void* intbuf;
^
= NULL
H5D.c:410:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:407:16: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
^
H5D.c:518:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tenum_insert (enumtype, st, &i);
^
H5D.c:528:24: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:525:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
^
H5D.c:606:24: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:603:20: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
^
H5D.c:622:24: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (superclass == H5T_FLOAT) {
^~~~~~~~~~~~~~~~~~~~~~~
H5D.c:628:98: 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:622:20: note: remove the 'if' if its condition is always true
} else if (superclass == H5T_FLOAT) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:615:24: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (superclass == H5T_FLOAT) {
^~~~~~~~~~~~~~~~~~~~~~~
H5D.c:628:98: 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:615:20: note: remove the 'if' if its condition is always true
} else if (superclass == H5T_FLOAT) {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:610:19: note: initialize the variable 'buf' to silence this warning
void * buf;
^
= NULL
H5D.c:712:11: warning: unused variable 'mem_type_id' [-Wunused-variable]
hid_t mem_type_id = -1;
^
H5D.c:834:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tclose(dtype_id);
^
24 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5G.c -o H5G.o
H5G.c:68:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Gget_info( group_id, &group_info );
^
H5G.c:116:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Gget_info_by_name( loc_id, group_name, &group_info, H5P_DEFAULT );
^
H5G.c:167:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Gget_info_by_idx( loc_id, group_name, index_type, order, n, &group_info, H5P_DEFAULT );
^
3 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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/4.0/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/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5S.c -o H5S.o
H5S.c:223:10: warning: unused variable 'j' [-Wunused-variable]
int i, j;
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c h5dump.c -o h5dump.o
h5dump.c:68:29: warning: unused variable 'idx' [-Wunused-variable]
hsize_t idx=0;
^
h5dump.c:245:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToDumpTree, &data );
^
2 warnings generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I/usr/local/include -fPIC -Wall -g -O2 -c h5ls.c -o h5ls.o
h5ls.c:58:29: warning: unused variable 'idx' [-Wunused-variable]
hsize_t idx=0;
^
1 warning generated.
clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.0/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/4.0/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/4.0/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/4.0/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/4.0/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++11 -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 H5T.o H5Z.o H5constants.o HandleList.o HandleListWrap.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.12-bioc/meat/rhdf5.buildbin-libdir/00LOCK-rhdf5/00new/rhdf5/libs
** R
** 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 (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/4.0/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/4.0/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/4.0/Resources/lib/libquadmath.0.dylib" "rhdf5.buildbin-libdir/rhdf5/libs/rhdf5.so"
