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### Running command:
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### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL rhdf5
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* installing to library ‘/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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_STRING’:
H5A.c:245:12: warning: unused variable ‘herr’ [-Wunused-variable]
245 | herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
| ^~~~
H5A.c: In function ‘H5Aread_helper_INTEGER’:
H5A.c:206:9: warning: ‘Rval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
206 | return(Rval);
| ^
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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:183:20: warning: unused variable ‘status’ [-Wunused-variable]
183 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
| ^~~~~~
H5D.c:180:18: warning: unused variable ‘status’ [-Wunused-variable]
180 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
| ^~~~~~
H5D.c:216:24: warning: unused variable ‘status’ [-Wunused-variable]
216 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
| ^~~~~~
H5D.c:213:20: warning: unused variable ‘status’ [-Wunused-variable]
213 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
| ^~~~~~
H5D.c:265:24: warning: unused variable ‘status’ [-Wunused-variable]
265 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
| ^~~~~~
H5D.c:262:20: warning: unused variable ‘status’ [-Wunused-variable]
262 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
| ^~~~~~
H5D.c: In function ‘H5Dread_helper_FLOAT’:
H5D.c:358:20: warning: unused variable ‘status’ [-Wunused-variable]
358 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
| ^~~~~~
H5D.c:355:16: warning: unused variable ‘status’ [-Wunused-variable]
355 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
| ^~~~~~
H5D.c: In function ‘H5Dread_helper_ENUM’:
H5D.c:466:20: warning: unused variable ‘status’ [-Wunused-variable]
466 | herr_t status = H5Tenum_insert (enumtype, st, &i);
| ^~~~~~
H5D.c:476:24: warning: unused variable ‘status’ [-Wunused-variable]
476 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
| ^~~~~~
H5D.c:473:20: warning: unused variable ‘status’ [-Wunused-variable]
473 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
| ^~~~~~
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:554:24: warning: unused variable ‘status’ [-Wunused-variable]
554 | herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
| ^~~~~~
H5D.c:551:20: warning: unused variable ‘status’ [-Wunused-variable]
551 | herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
| ^~~~~~
H5D.c: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:660:11: warning: unused variable ‘mem_type_id’ [-Wunused-variable]
660 | hid_t mem_type_id = -1;
| ^~~~~~~~~~~
H5D.c: In function ‘H5Dread_helper’:
H5D.c:782:12: warning: unused variable ‘status’ [-Wunused-variable]
782 | herr_t status = H5Tclose(dtype_id);
| ^~~~~~
H5D.c: In function ‘H5Dread_helper_INTEGER’:
H5D.c:318:21: warning: ‘intbuf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
318 | int64_to_integer64(intbuf, n, buf, sgn);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:264:38: warning: ‘dtypeNative’ may be used uninitialized in this function [-Wmaybe-uninitialized]
264 | hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:576:23: warning: ‘buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
576 | herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c:610:39: warning: ‘Rval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
610 | INTEGER(buffer)[li] = INTEGER(Rval)[lj];
| ^~~~~~~~~~~~~
H5D.c:553:38: warning: ‘arraytype’ may be used uninitialized in this function [-Wmaybe-uninitialized]
553 | hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(arraytype));
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include/R.h:75,
from H5E.h:4,
from H5E.c:1:
H5E.c: In function ‘custom_print_cb’:
/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5G.c -o H5G.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5Z.c -o H5Z.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c bit64conversion.c -o bit64conversion.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5dump.c -o h5dump.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5testLock.c -o h5testLock.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.14-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-3.14-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 bit64conversion.o external_filters.o h5dump.o h5ls.o h5testLock.o h5writeDataFrame.o printdatatype.o utils.o wrap.o /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.14-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-bioc/R/library/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)
