rhdf5 2.24.0
Mike Smith
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/rhdf5 |
| Branch: RELEASE_3_7 |
| Last Commit: e926e8c |
| Last Changed Date: 2018-04-30 10:35:23 -0400 (Mon, 30 Apr 2018) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | [ OK ] | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL rhdf5
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘rhdf5’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-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:153:10: 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:186:10: 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:213:12: warning: unused variable ‘herr’ [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
H5A.c:220:12: warning: unused variable ‘herr’ [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-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:271:9: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:268:14: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:283:12: 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:322:9: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:319:14: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
^
H5D.c:327:12: 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:494:14: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:491:12: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
^
H5D.c:506:10: 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: In function ‘H5Dread_helper_STRING’:
H5D.c:532:14: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:529:12: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtype_id);
^
H5D.c:540:12: warning: unused variable ‘herr’ [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, bufSTR );
^
H5D.c:550:12: warning: unused variable ‘herr’ [-Wunused-variable]
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, bufSTR );
^
H5D.c: In function ‘H5Dread_helper_ENUM’:
H5D.c:588:14: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tenum_insert (enumtype, st, &i);
^
H5D.c:599:9: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:596:14: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
^
H5D.c:614:12: 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: In function ‘H5Dread_helper_ARRAY’:
H5D.c:674:13: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:671:14: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
^
H5D.c:696:12: 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: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:777:9: warning: unused variable ‘mem_type_id’ [-Wunused-variable]
hid_t mem_type_id = -1;
^
H5D.c: In function ‘H5Dread_helper_INTEGER’:
H5D.c:442:40: warning: ‘intbuf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (((unsigned long long *)intbuf)[i] > LLONG_MAX) {
^
H5D.c:321:23: warning: ‘dtypeNative’ may be used uninitialized in this function [-Wmaybe-uninitialized]
hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative));
^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-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-3.7-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-3.7-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:76:3: note: in expansion of macro ‘error’
error:
^
H5E.c: In function ‘custom_print_cb_compact’:
/home/biocbuild/bbs-3.7-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:112:3: note: in expansion of macro ‘error’
error:
^
H5E.c:87:16: warning: unused variable ‘indent’ [-Wunused-variable]
const int indent = 4;
^
H5E.c: In function ‘_rhdf5PrintErrorR’:
H5E.c:121:12: warning: unused variable ‘eee’ [-Wunused-variable]
herr_t eee = H5Ewalk(estack_id, H5E_WALK_DOWNWARD, &custom_print_cb, &client_data);
^
H5E.c: In function ‘_rhdf5PrintErrorRcompact’:
H5E.c:153:12: warning: unused variable ‘eee’ [-Wunused-variable]
herr_t eee = H5Ewalk(estack_id, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data);
^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-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:66:10: 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:113:10: 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:163:10: 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-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o
H5P.c: In function ‘_H5Pset_libver_bounds’:
H5P.c:689:16: warning: unused variable ‘libver_high’ [-Wunused-variable]
H5F_libver_t libver_high = INTEGER(_libver_high)[0];
^
H5P.c:688:16: warning: unused variable ‘libver_low’ [-Wunused-variable]
H5F_libver_t libver_low = INTEGER(_libver_low)[0];
^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5S.c -o H5S.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o
In file included from /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include/hdf5.h:37:0,
from myhdf5.h:7,
from H5G.h:8,
from H5constants.c:1:
H5constants.c: In function ‘_H5constants’:
/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include/H5Spublic.h:26:23: warning: overflow in implicit constant conversion [-Woverflow]
#define H5S_UNLIMITED ((hsize_t)(hssize_t)(-1))
^
H5constants.c:62:71: note: in expansion of macro ‘H5S_UNLIMITED’
int const_H5S[4] = { H5S_SCALAR, H5S_SIMPLE, H5S_NULL, H5S_UNLIMITED };
^
g++ -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c h5dump.c -o h5dump.o
h5dump.c: In function ‘_h5dump’:
h5dump.c:331:12: warning: unused variable ‘herr’ [-Wunused-variable]
herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToLinfoTree, &data );
^
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-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-3.7-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c wrap.c -o wrap.o
g++ -shared -L/home/biocbuild/bbs-3.7-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 H5constants.o HandleList.o HandleListWrap.o h5dump.o h5ls.o h5writeDataFrame.o printdatatype.o wrap.o /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.7-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/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
* DONE (rhdf5)