############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL rhdf5 ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘rhdf5’ ... ** using staged installation configure: creating ./config.status config.status: creating src/external_filters.h ** libs gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5A.c -o H5A.o H5A.c: In function ‘H5Aread_helper_INTEGER’: H5A.c:142:10: warning: unused variable ‘herr’ [-Wunused-variable] 142 | herr_t herr = H5Aread(attr_id, mem_type_id, buf ); | ^~~~ H5A.c: In function ‘H5Aread_helper_FLOAT’: H5A.c:175:10: warning: unused variable ‘herr’ [-Wunused-variable] 175 | herr_t herr = H5Aread(attr_id, mem_type_id, buf ); | ^~~~ H5A.c: In function ‘H5Aread_helper_STRING’: H5A.c:202:12: warning: unused variable ‘herr’ [-Wunused-variable] 202 | herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR ); | ^~~~ H5A.c:209:12: warning: unused variable ‘herr’ [-Wunused-variable] 209 | herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR ); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5D.c -o H5D.o H5D.c: In function ‘H5Dread_helper_INTEGER’: H5D.c:154:20: warning: unused variable ‘status’ [-Wunused-variable] 154 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:151:18: warning: unused variable ‘status’ [-Wunused-variable] 151 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_UCHAR); | ^~~~~~ H5D.c:166:16: warning: unused variable ‘herr’ [-Wunused-variable] 166 | 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] 179 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:176:18: warning: unused variable ‘status’ [-Wunused-variable] 176 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32); | ^~~~~~ H5D.c:190:16: warning: unused variable ‘herr’ [-Wunused-variable] 190 | 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] 208 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:205:20: warning: unused variable ‘status’ [-Wunused-variable] 205 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32); | ^~~~~~ H5D.c:220:16: warning: unused variable ‘herr’ [-Wunused-variable] 220 | 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] 254 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:251:20: warning: unused variable ‘status’ [-Wunused-variable] 251 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative); | ^~~~~~ H5D.c:259:16: warning: unused variable ‘herr’ [-Wunused-variable] 259 | herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, intbuf ); | ^~~~ H5D.c: In function ‘H5Dread_helper_FLOAT’: H5D.c:410:20: warning: unused variable ‘status’ [-Wunused-variable] 410 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:407:16: warning: unused variable ‘status’ [-Wunused-variable] 407 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE); | ^~~~~~ H5D.c: In function ‘H5Dread_helper_ENUM’: H5D.c:518:20: warning: unused variable ‘status’ [-Wunused-variable] 518 | herr_t status = H5Tenum_insert (enumtype, st, &i); | ^~~~~~ H5D.c:528:24: warning: unused variable ‘status’ [-Wunused-variable] 528 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:525:20: warning: unused variable ‘status’ [-Wunused-variable] 525 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype); | ^~~~~~ H5D.c: In function ‘H5Dread_helper_ARRAY’: H5D.c:606:24: warning: unused variable ‘status’ [-Wunused-variable] 606 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id); | ^~~~~~ H5D.c:603:20: warning: unused variable ‘status’ [-Wunused-variable] 603 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype); | ^~~~~~ H5D.c: In function ‘H5Dread_helper_COMPOUND’: H5D.c:712:11: warning: unused variable ‘mem_type_id’ [-Wunused-variable] 712 | hid_t mem_type_id = -1; | ^~~~~~~~~~~ H5D.c: In function ‘H5Dread_helper’: H5D.c:834:12: warning: unused variable ‘status’ [-Wunused-variable] 834 | herr_t status = H5Tclose(dtype_id); | ^~~~~~ H5D.c: In function ‘H5Dread_helper_INTEGER’: H5D.c:366:59: warning: ‘intbuf’ may be used uninitialized in this function [-Wmaybe-uninitialized] 366 | if (((unsigned long long *)intbuf)[i] > LLONG_MAX) { | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~ H5D.c:253:38: warning: ‘dtypeNative’ may be used uninitialized in this function [-Wmaybe-uninitialized] 253 | hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ H5D.c: In function ‘H5Dread_helper_ARRAY’: H5D.c:628:23: warning: ‘buf’ may be used uninitialized in this function [-Wmaybe-uninitialized] 628 | herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf ); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ H5D.c:662:39: warning: ‘Rval’ may be used uninitialized in this function [-Wmaybe-uninitialized] 662 | INTEGER(buffer)[li] = INTEGER(Rval)[lj]; | ^~~~~~~~~~~~~ H5D.c:605:38: warning: ‘arraytype’ may be used uninitialized in this function [-Wmaybe-uninitialized] 605 | hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(arraytype)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5E.c -o H5E.o In file included from /home/biocbuild/bbs-3.13-bioc/R/include/R.h:86, from H5E.h:4, from H5E.c:1: H5E.c: In function ‘custom_print_cb’: /home/biocbuild/bbs-3.13-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label] 52 | #define error Rf_error | ^~~~~~~~ H5E.c:66:5: note: in expansion of macro ‘error’ 66 | error: | ^~~~~ H5E.c: In function ‘custom_print_cb_compact’: /home/biocbuild/bbs-3.13-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label] 52 | #define error Rf_error | ^~~~~~~~ H5E.c:98:5: note: in expansion of macro ‘error’ 98 | error: | ^~~~~ H5E.c:75:15: warning: unused variable ‘indent’ [-Wunused-variable] 75 | const int indent = 4; | ^~~~~~ H5E.c: In function ‘_rhdf5PrintErrorR’: H5E.c:110:16: warning: unused variable ‘eee’ [-Wunused-variable] 110 | herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb, &client_data); | ^~~ H5E.c: In function ‘_rhdf5PrintErrorRcompact’: H5E.c:141:16: warning: unused variable ‘eee’ [-Wunused-variable] 141 | herr_t eee = H5Ewalk(estack_id_copy, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data); | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5G.c -o H5G.o H5G.c: In function ‘_H5Gget_info’: H5G.c:68:10: warning: unused variable ‘herr’ [-Wunused-variable] 68 | herr_t herr = H5Gget_info( group_id, &group_info ); | ^~~~ H5G.c: In function ‘_H5Gget_info_by_name’: H5G.c:116:10: warning: unused variable ‘herr’ [-Wunused-variable] 116 | herr_t herr = H5Gget_info_by_name( loc_id, group_name, &group_info, H5P_DEFAULT ); | ^~~~ H5G.c: In function ‘_H5Gget_info_by_idx’: H5G.c:167:10: warning: unused variable ‘herr’ [-Wunused-variable] 167 | herr_t herr = H5Gget_info_by_idx( loc_id, group_name, index_type, order, n, &group_info, H5P_DEFAULT ); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5O.c -o H5O.o H5O.c: In function ‘H5Oget_num_attrs’: H5O.c:13:10: warning: unused variable ‘herr’ [-Wunused-variable] 13 | herr_t herr = H5Aiterate( obj_id, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &idx, &opAcount, &n); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S.c -o H5S.o H5S.c: In function ‘_H5Sselect_hyperslab’: H5S.c:258:12: warning: unused variable ‘herr’ [-Wunused-variable] 258 | herr_t herr = H5Sselect_hyperslab( space_id, op, start, stride, count, block ); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S_extras.c -o H5S_extras.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5Z.c -o H5Z.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o g++ -std=gnu++14 -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o HandleListWrap.c: In function ‘_h5listOpenObjects’: HandleListWrap.c:138:12: warning: variable ‘status’ set but not used [-Wunused-but-set-variable] 138 | herr_t status; | ^~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c external_filters.c -o external_filters.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5dump.c -o h5dump.o h5dump.c: In function ‘opAddToDumpTree’: h5dump.c:68:29: warning: unused variable ‘idx’ [-Wunused-variable] 68 | hsize_t idx=0; | ^~~ h5dump.c: In function ‘_h5dump’: h5dump.c:245:12: warning: unused variable ‘herr’ [-Wunused-variable] 245 | herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToDumpTree, &data ); | ^~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o h5ls.c: In function ‘opAddToObjList’: h5ls.c:58:29: warning: unused variable ‘idx’ [-Wunused-variable] 58 | hsize_t idx=0; | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5testLock.c -o h5testLock.o h5testLock.c: In function ‘_h5fileLock’: h5testLock.c:9:7: warning: variable ‘lk2’ set but not used [-Wunused-but-set-variable] 9 | int lk2 = -1; | ^~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c printdatatype.c -o printdatatype.o printdatatype.c: In function ‘getDatatypeName’: printdatatype.c:21:16: warning: variable ‘sign_s’ set but not used [-Wunused-but-set-variable] 21 | const char *sign_s=NULL; /* sign scheme string */ | ^~~~~~ printdatatype.c:19:16: warning: variable ‘order_s’ set but not used [-Wunused-but-set-variable] 19 | const char *order_s=NULL; /* byte order string */ | ^~~~~~~ gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o gcc -I"/home/biocbuild/bbs-3.13-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c wrap.c -o wrap.o g++ -std=gnu++14 -shared -L/home/biocbuild/bbs-3.13-bioc/R/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 /home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.13-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.13-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.13-bioc/R/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)