############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL rhdf5 ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * 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: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/4.1/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: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/4.1/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 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/4.1/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 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 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/4.1/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/4.1/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 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 /Library/Frameworks/R.framework/Versions/4.1/Resources/library/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)