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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### rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh rhdf5_2.26.2.tar.gz /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R rhdf5.buildbin-libdir
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>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=rhdf5.buildbin-libdir rhdf5_2.26.2.tar.gz'
>>>>>>>
* installing *source* package ‘rhdf5’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5.c -o H5.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5A.c -o H5A.o
H5A.c:166:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, buf );
^
H5A.c:199:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Aread(attr_id, mem_type_id, buf );
^
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 );
^
4 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5D.c -o H5D.o
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:315:20: warning: variable 'intbuf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:319:13: note: uninitialized use occurs here
if (intbuf == 0) {
^˜˜˜˜˜
H5D.c:315:16: note: remove the 'if' if its condition is always true
} else if ((b == 8) & (sgn == H5T_SGN_NONE)) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:305:21: note: initialize the variable 'intbuf' to silence this warning
void* intbuf;
^
= NULL
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: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: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: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:694:24: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (superclass == H5T_FLOAT) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:700:98: note: uninitialized use occurs here
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^˜˜
H5D.c:694:20: note: remove the 'if' if its condition is always true
} else if (superclass == H5T_FLOAT) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:687:24: warning: variable 'buf' is used uninitialized whenever 'if' condition is false [-Wsometimes-uninitialized]
} else if (superclass == H5T_FLOAT) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:700:98: note: uninitialized use occurs here
herr_t herr = H5Dread(dataset_id, mem_type_id, mem_space_id, file_space_id, H5P_DEFAULT, buf );
^˜˜
H5D.c:687:20: note: remove the 'if' if its condition is always true
} else if (superclass == H5T_FLOAT) {
^˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜˜
H5D.c:682:19: note: initialize the variable 'buf' to silence this warning
void * buf;
^
= NULL
H5D.c:781:11: warning: unused variable 'mem_type_id' [-Wunused-variable]
hid_t mem_type_id = -1;
^
24 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5E.c -o H5E.o
H5E.c:76:3: warning: unused label 'Rf_error' [-Wunused-label]
error:
^˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:52:15: note: expanded from macro 'error'
#define error Rf_error
^
H5E.c:87:16: warning: unused variable 'indent' [-Wunused-variable]
const int indent = 4;
^
H5E.c:112:3: warning: unused label 'Rf_error' [-Wunused-label]
error:
^˜˜˜˜˜
/Library/Frameworks/R.framework/Resources/include/R_ext/Error.h:52:15: note: expanded from macro 'error'
#define error Rf_error
^
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:153:12: warning: unused variable 'eee' [-Wunused-variable]
herr_t eee = H5Ewalk(estack_id, H5E_WALK_DOWNWARD, &custom_print_cb_compact, &client_data);
^
5 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5F.c -o H5F.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5G.c -o H5G.o
H5G.c:68:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Gget_info( group_id, &group_info );
^
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: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 );
^
3 warnings generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5I.c -o H5I.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5L.c -o H5L.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5O.c -o H5O.o
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);
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5P.c -o H5P.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5S.c -o H5S.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5T.c -o H5T.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c H5constants.c -o H5constants.o
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c HandleList.cpp -o HandleList.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c HandleListWrap.c -o HandleListWrap.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c h5dump.c -o h5dump.o
h5dump.c:332:12: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToLinfoTree, &data );
^
1 warning generated.
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c h5ls.c -o h5ls.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c h5testLock.c -o h5testLock.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c h5writeDataFrame.c -o h5writeDataFrame.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c printdatatype.c -o printdatatype.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/include" -I/usr/local/include -fPIC -Wall -g -O2 -c wrap.c -o wrap.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/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 /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/3.5/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.8-bioc/meat/rhdf5.buildbin-libdir/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)
>>>>>>>
>>>>>>> FIXING LINKS FOR rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so
>>>>>>>
install_name_tool -change "/usr/local/lib/libgcc_s.1.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgcc_s.1.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"
install_name_tool -change "/usr/local/lib/libgfortran.3.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"
install_name_tool -change "/usr/local/lib/libreadline.5.2.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.5.2.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"
install_name_tool -change "/usr/local/lib/libreadline.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libreadline.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"
install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libquadmath.0.dylib" "rhdf5.buildbin-libdir/rhdf5/libs//rhdf5.so"