This page was generated on 2019-04-16 11:49:29 -0400 (Tue, 16 Apr 2019).
rhdf5 2.26.2 Mike Smith
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
URL: https://git.bioconductor.org/packages/rhdf5 |
Branch: RELEASE_3_8 |
Last Commit: 81e1125 |
Last Changed Date: 2019-01-02 10:53:12 -0400 (Wed, 02 Jan 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | |
merida1 | 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-3.8-bioc/R/bin/R CMD INSTALL rhdf5
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘rhdf5’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5.c -o H5.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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:166:10: 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:199:10: 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:226:12: warning: unused variable ‘herr’ [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
H5A.c:233:12: warning: unused variable ‘herr’ [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, bufSTR );
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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:278:24: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:275:20: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:290:16: 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:329:24: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:326:20: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
^
H5D.c:334:16: 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:500:20: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:497:16: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
^
H5D.c:512:12: 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_STRING’:
H5D.c:538:20: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:535:16: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtype_id);
^
H5D.c:546:16: 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:556:16: 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:592:20: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tenum_insert (enumtype, st, &i);
^
H5D.c:603:24: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:600:20: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
^
H5D.c:618:16: 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: In function ‘H5Dread_helper_ARRAY’:
H5D.c:678:24: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:675:20: warning: unused variable ‘status’ [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
^
H5D.c:700:16: 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: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:781:11: warning: unused variable ‘mem_type_id’ [-Wunused-variable]
hid_t mem_type_id = -1;
^
H5D.c: In function ‘H5Dread_helper_INTEGER’:
H5D.c:449:59: warning: ‘intbuf’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if (((unsigned long long *)intbuf)[i] > LLONG_MAX) {
^
H5D.c:328:38: 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:700:16: 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:731:39: warning: ‘Rval’ may be used uninitialized in this function [-Wmaybe-uninitialized]
INTEGER(buffer)[li] = INTEGER(Rval)[lj];
^
H5D.c:677:38: 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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-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-3.8-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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5F.c -o H5F.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5I.c -o H5I.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5L.c -o H5L.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5P.c -o H5P.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5S.c -o H5S.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5T.c -o H5T.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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:332:12: 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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/include" -I/usr/local/include -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-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-3.8-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 h5testLock.o h5writeDataFrame.o printdatatype.o wrap.o /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-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)