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### Running command:
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### /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL rhdf5
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* 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
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
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]
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]
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 );
^~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
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: In function ‘H5Dread_helper_FLOAT’:
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: In function ‘H5Dread_helper_ENUM’:
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: In function ‘H5Dread_helper_ARRAY’:
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: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:712:11: warning: unused variable ‘mem_type_id’ [-Wunused-variable]
hid_t mem_type_id = -1;
^~~~~~~~~~~
H5D.c: In function ‘H5Dread_helper’:
H5D.c:834:12: warning: unused variable ‘status’ [-Wunused-variable]
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]
if (((unsigned long long *)intbuf)[i] > LLONG_MAX) {
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
H5D.c:253:38: warning: ‘dtypeNative’ may be used uninitialized in this function [-Wmaybe-uninitialized]
hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:628:16: warning: ‘buf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
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]
INTEGER(buffer)[li] = INTEGER(Rval)[lj];
^~~~~~~~~~~~~
H5D.c:605:38: warning: ‘arraytype’ may be used uninitialized in this function [-Wmaybe-uninitialized]
hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(arraytype));
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include/R.h:86:0,
from H5E.h:4,
from H5E.c:1:
H5E.c: In function ‘custom_print_cb’:
/home/biocbuild/bbs-3.12-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label]
#define error Rf_error
^
H5E.c:66:5: note: in expansion of macro ‘error’
error:
^~~~~
H5E.c: In function ‘custom_print_cb_compact’:
/home/biocbuild/bbs-3.12-bioc/R/include/R_ext/Error.h:52:15: warning: label ‘Rf_error’ defined but not used [-Wunused-label]
#define error Rf_error
^
H5E.c:98:5: note: in expansion of macro ‘error’
error:
^~~~~
H5E.c:75:15: warning: unused variable ‘indent’ [-Wunused-variable]
const int indent = 4;
^~~~~~
H5E.c: In function ‘_rhdf5PrintErrorR’:
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: In function ‘_rhdf5PrintErrorRcompact’:
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);
^~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
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]
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]
herr_t herr = H5Gget_info_by_idx( loc_id, group_name, index_type, order, n, &group_info, H5P_DEFAULT );
^~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
herr_t herr = H5Aiterate( obj_id, H5_INDEX_CRT_ORDER, H5_ITER_NATIVE, &idx, &opAcount, &n);
^~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5S.c -o H5S.o
H5S.c: In function ‘_H5Sselect_cols’:
H5S.c:223:10: warning: unused variable ‘j’ [-Wunused-variable]
int i, j;
^
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5Z.c -o H5Z.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
herr_t status;
^~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
hsize_t idx=0;
^~~
h5dump.c: In function ‘_h5dump’:
h5dump.c:245:12: warning: unused variable ‘herr’ [-Wunused-variable]
herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToDumpTree, &data );
^~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
hsize_t idx=0;
^~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
int lk2 = -1;
^~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-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]
const char *sign_s=NULL; /* sign scheme string */
^~~~~~
printdatatype.c:19:16: warning: variable ‘order_s’ set but not used [-Wunused-but-set-variable]
const char *order_s=NULL; /* byte order string */
^~~~~~~
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c utils.c -o utils.o
gcc -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -Wall -c wrap.c -o wrap.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-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 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-3.12-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.12-bioc/R/library/Rhdf5lib/lib/libsz.a -lcrypto -lcurl -lz -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-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)
