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###
### Running command:
###
### rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.6/bioc/src/contrib/rhdf5_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --library=rhdf5.buildbin-libdir --merge-multiarch rhdf5_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL rhdf5_2.22.0.zip && rm rhdf5_2.22.0.tar.gz rhdf5_2.22.0.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 5168k 100 5168k 0 0 75.1M 0 --:--:-- --:--:-- --:--:-- 78.8M
install for i386
* installing *source* package 'rhdf5' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
cp includeWin/i386/* includeWin/
cp libwin/i386/*.dll .
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5.c -o H5.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -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 );
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5D.c -o H5D.o
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:220:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:217:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:232:12: 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:268:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:265:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
^
H5D.c:273:12: 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:438:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:435:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
^
H5D.c:450:10: 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:471:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:468:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtype_id);
^
H5D.c:479:12: 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:490:12: 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:525:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tenum_insert (enumtype, st, &i);
^
H5D.c:536:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:533:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
^
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, buf );
^
H5D.c: In function 'H5Dread_helper_ARRAY':
H5D.c:603:13: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:600:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
^
H5D.c:625:12: 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:660:9: warning: unused variable 'mem_type_id' [-Wunused-variable]
hid_t mem_type_id = -1;
^
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:388:40: warning: 'intbuf' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (((unsigned long long *)intbuf)[i] > LLONG_MAX) {
^
H5D.c:267:23: warning: 'dtypeNative' may be used uninitialized in this function [-Wmaybe-uninitialized]
hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative));
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5E.c -o H5E.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:86:0,
from H5E.h:4,
from H5E.c:1:
H5E.c: In function 'custom_print_cb':
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/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':
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/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);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5F.c -o H5F.o
H5F.c: In function '_H5Fget_name':
H5F.c:116:33: warning: passing argument 2 of 'H5Fget_name' from incompatible pointer type
size = H5Fget_name( obj_id, &name, size+1);
^
In file included from includeWin/hdf5.h:29:0,
from myhdf5.h:5,
from H5F.h:8,
from H5F.c:1:
includeWin/H5Fpublic.h:174:16: note: expected 'char *' but argument is of type 'char (*)[(sizetype)((int)size + 1)]'
H5_DLL ssize_t H5Fget_name(hid_t obj_id, char *name, size_t size);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -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 );
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5I.c -o H5I.o
H5I.c: In function '_H5Iget_name':
H5I.c:24:24: warning: passing argument 2 of 'H5Iget_name' from incompatible pointer type
H5Iget_name( obj_id, &name, st+1 );
^
In file included from includeWin/H5Apublic.h:23:0,
from includeWin/hdf5.h:25,
from myhdf5.h:5,
from H5I.h:8,
from H5I.c:1:
includeWin/H5Ipublic.h:85:16: note: expected 'char *' but argument is of type 'char (*)[(sizetype)((int)st + 1)]'
H5_DLL ssize_t H5Iget_name(hid_t id, char *name/*out*/, size_t size);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5L.c -o H5L.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -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);
^
H5O.c: In function '_H5Oopen':
H5O.c:56:3: warning: implicit declaration of function 'addHandle' [-Wimplicit-function-declaration]
addHandle(hid);
^
H5O.c: In function '_H5Oclose':
H5O.c:69:5: warning: implicit declaration of function 'removeHandle' [-Wimplicit-function-declaration]
removeHandle(object_id);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -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];
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5S.c -o H5S.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5T.c -o H5T.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c H5constants.c -o H5constants.o
C:/Rtools/mingw_32/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -mtune=generic -c HandleList.cpp -o HandleList.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c HandleListWrap.c -o HandleListWrap.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c h5dump.c -o h5dump.o
h5dump.c: In function 'opAddToLinfoTree':
h5dump.c:85:3: warning: implicit declaration of function 'H5Oget_num_attrs' [-Wimplicit-function-declaration]
newElement->num_attrs = H5Oget_num_attrs(oid);
^
h5dump.c:114:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%lu", size[newElement->rank-1]);
^
h5dump.c:116:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, size[i]);
^
h5dump.c:124:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%lu", maxsize[newElement->rank-1]);
^
h5dump.c:126:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, maxsize[i]);
^
h5dump.c: In function '_h5dump':
h5dump.c:314:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToLinfoTree, &data );
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c h5ls.c -o h5ls.o
h5ls.c: In function 'opAddToLinfoList':
h5ls.c:99:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%lu", size[newElement->rank-1]);
^
h5ls.c:101:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, size[i]);
^
h5ls.c:109:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%lu", maxsize[newElement->rank-1]);
^
h5ls.c:111:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, maxsize[i]);
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c h5writeDataFrame.c -o h5writeDataFrame.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -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 */
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=generic -c wrap.c -o wrap.o
C:\Rtools\mingw_32\bin\nm.exe: 'libhdf5ForBioC': No such file
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o rhdf5.dll tmp.def 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 -llibhdf5ForBioC-7 -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -llibsz-2 -lm -L. -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
converting help for package 'rhdf5'
finding HTML links ... done
H5 html
H5A html
H5D html
H5F html
H5G html
H5I html
H5IdComponent-class html
H5L html
H5O html
H5P html
H5P_DATASET_ACCESS html
H5P_DATASET_CREATE html
H5P_LINK_CREATE html
H5S html
H5T html
h5const html
h5createAttribute html
h5createDataset html
h5createFile html
h5createGroup html
h5errorHandling html
h5listIdentifier html
h5ls html
h5save html
h5set_extent html
h5version html
h5write html
methods-And html
methods-Dollar1 html
methods-Dollar2 html
methods-subset1 html
methods-subset2 html
rhdf5 html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'rhdf5' ...
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
** libs
cp includeWin/x64/* includeWin/
cp libwin/x64/*.dll .
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5.c -o H5.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -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 );
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5D.c -o H5D.o
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:220:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:217:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_INT32);
^
H5D.c:232:12: 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:268:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:265:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtypeNative);
^
H5D.c:273:12: 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:438:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:435:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, H5T_NATIVE_DOUBLE);
^
H5D.c:450:10: 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:471:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:468:12: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, dtype_id);
^
H5D.c:479:12: 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:490:12: 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:525:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tenum_insert (enumtype, st, &i);
^
H5D.c:536:9: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:533:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, enumtype);
^
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, buf );
^
H5D.c: In function 'H5Dread_helper_ARRAY':
H5D.c:603:13: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id2, cpdField[i], 0, mem_type_id);
^
H5D.c:600:14: warning: unused variable 'status' [-Wunused-variable]
herr_t status = H5Tinsert(mem_type_id, cpdField[0], 0, arraytype);
^
H5D.c:625:12: 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:660:9: warning: unused variable 'mem_type_id' [-Wunused-variable]
hid_t mem_type_id = -1;
^
H5D.c: In function 'H5Dread_helper_INTEGER':
H5D.c:388:40: warning: 'intbuf' may be used uninitialized in this function [-Wmaybe-uninitialized]
if (((unsigned long long *)intbuf)[i] > LLONG_MAX) {
^
H5D.c:267:23: warning: 'dtypeNative' may be used uninitialized in this function [-Wmaybe-uninitialized]
hid_t mem_type_id2 = H5Tcreate(H5T_COMPOUND, H5Tget_size(dtypeNative));
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5E.c -o H5E.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include/R.h:86:0,
from H5E.h:4,
from H5E.c:1:
H5E.c: In function 'custom_print_cb':
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/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':
C:/Users/BIOCBU˜1/BBS-3˜1.6-B/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);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5F.c -o H5F.o
H5F.c: In function '_H5Fget_name':
H5F.c:116:33: warning: passing argument 2 of 'H5Fget_name' from incompatible pointer type
size = H5Fget_name( obj_id, &name, size+1);
^
In file included from includeWin/hdf5.h:29:0,
from myhdf5.h:5,
from H5F.h:8,
from H5F.c:1:
includeWin/H5Fpublic.h:174:16: note: expected 'char *' but argument is of type 'char (*)[(sizetype)(size + 1ll)]'
H5_DLL ssize_t H5Fget_name(hid_t obj_id, char *name, size_t size);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -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 );
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5I.c -o H5I.o
H5I.c: In function '_H5Iget_name':
H5I.c:24:24: warning: passing argument 2 of 'H5Iget_name' from incompatible pointer type
H5Iget_name( obj_id, &name, st+1 );
^
In file included from includeWin/H5Apublic.h:23:0,
from includeWin/hdf5.h:25,
from myhdf5.h:5,
from H5I.h:8,
from H5I.c:1:
includeWin/H5Ipublic.h:85:16: note: expected 'char *' but argument is of type 'char (*)[(sizetype)(st + 1ll)]'
H5_DLL ssize_t H5Iget_name(hid_t id, char *name/*out*/, size_t size);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5L.c -o H5L.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -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);
^
H5O.c: In function '_H5Oopen':
H5O.c:56:3: warning: implicit declaration of function 'addHandle' [-Wimplicit-function-declaration]
addHandle(hid);
^
H5O.c: In function '_H5Oclose':
H5O.c:69:5: warning: implicit declaration of function 'removeHandle' [-Wimplicit-function-declaration]
removeHandle(object_id);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -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];
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5S.c -o H5S.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5T.c -o H5T.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c H5constants.c -o H5constants.o
C:/Rtools/mingw_64/bin/g++ -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -mtune=generic -c HandleList.cpp -o HandleList.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c HandleListWrap.c -o HandleListWrap.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c h5dump.c -o h5dump.o
h5dump.c: In function 'opAddToLinfoTree':
h5dump.c:85:3: warning: implicit declaration of function 'H5Oget_num_attrs' [-Wimplicit-function-declaration]
newElement->num_attrs = H5Oget_num_attrs(oid);
^
h5dump.c:114:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%lu", size[newElement->rank-1]);
^
h5dump.c:116:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, size[i]);
^
h5dump.c:124:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%lu", maxsize[newElement->rank-1]);
^
h5dump.c:126:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, maxsize[i]);
^
h5dump.c: In function '_h5dump':
h5dump.c:314:10: warning: unused variable 'herr' [-Wunused-variable]
herr_t herr = H5Literate( loc_id, data.index_type, data.order, &idx, &opAddToLinfoTree, &data );
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c h5ls.c -o h5ls.o
h5ls.c: In function 'opAddToLinfoList':
h5ls.c:99:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%lu", size[newElement->rank-1]);
^
h5ls.c:101:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, size[i]);
^
h5ls.c:109:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%lu", maxsize[newElement->rank-1]);
^
h5ls.c:111:6: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, maxsize[i]);
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c h5writeDataFrame.c -o h5writeDataFrame.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -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 */
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/include" -DNDEBUG -I"C:/local323/include" -I"C:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=generic -c wrap.c -o wrap.o
C:\Rtools\mingw_64\bin\nm.exe: 'libhdf5ForBioC': No such file
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o rhdf5.dll tmp.def 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 -llibhdf5ForBioC-7 -LC:/Users/biocbuild/bbs-3.6-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -llibsz-2 -lm -L. -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.6-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.6-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5' as rhdf5_2.22.0.zip
* DONE (rhdf5)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.6-bioc/R/library'
package 'rhdf5' successfully unpacked and MD5 sums checked
In R CMD INSTALL
