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BioC 3.4: INSTALL report for rhdf5 on tokay1

This page was generated on 2017-04-15 16:17:03 -0400 (Sat, 15 Apr 2017).

Package 1046/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rhdf5 2.18.0
Bernd Fischer
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/rhdf5
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rhdf5
Version: 2.18.0
Command: rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir && C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.4/bioc/src/contrib/rhdf5_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=rhdf5.buildbin-libdir --merge-multiarch rhdf5_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL rhdf5_2.18.0.zip && rm rhdf5_2.18.0.tar.gz rhdf5_2.18.0.zip
StartedAt: 2017-04-14 18:09:25 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 18:10:33 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 67.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   rm -rf rhdf5.buildbin-libdir && mkdir rhdf5.buildbin-libdir  && C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.4/bioc/src/contrib/rhdf5_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --library=rhdf5.buildbin-libdir --merge-multiarch rhdf5_2.18.0.tar.gz && C:\Users\biocbuild\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL rhdf5_2.18.0.zip  && rm rhdf5_2.18.0.tar.gz rhdf5_2.18.0.zip
###
##############################################################################
##############################################################################


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100 5131k  100 5131k    0     0  5574k      0 --:--:-- --:--:-- --:--:-- 5571k

install for i386

* installing *source* package 'rhdf5' ...
** libs
cp includeWin/i386/* includeWin/
cp libwin/i386/*.dll .
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5.c -o H5.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5E.c -o H5E.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/R.h:79:0,
                 from H5E.h:4,
                 from H5E.c:1:
H5E.c: In function 'custom_print_cb':
C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5L.c -o H5L.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5S.c -o H5S.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5T.c -o H5T.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c H5constants.c -o H5constants.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c HandleList.cpp -o HandleList.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c HandleListWrap.c -o HandleListWrap.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -c h5writeDataFrame.c -o h5writeDataFrame.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O3 -Wall  -std=gnu99 -mtune=core2 -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-3.4-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -llibsz-2 -lm -L. -LC:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rhdf5' ...
** libs
cp includeWin/x64/* includeWin/
cp libwin/x64/*.dll .
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5.c -o H5.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5E.c -o H5E.o
In file included from C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include/R.h:79:0,
                 from H5E.h:4,
                 from H5E.c:1:
H5E.c: In function 'custom_print_cb':
C:/Users/BIOCBU˜1/BBS-3˜1.4-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˜1.4-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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5L.c -o H5L.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5S.c -o H5S.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5T.c -o H5T.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c H5constants.c -o H5constants.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -mtune=core2 -c HandleList.cpp -o HandleList.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c HandleListWrap.c -o HandleListWrap.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -c h5writeDataFrame.c -o h5writeDataFrame.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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˜1.4-B/R/include" -DNDEBUG     -I"C:/local323/include"  -I"C:/Users/biocbuild/bbs-3.4-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS   -O2 -Wall  -std=gnu99 -mtune=core2 -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-3.4-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -llibsz-2 -lm -L. -LC:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.4-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.4-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5' as rhdf5_2.18.0.zip
* DONE (rhdf5)
* installing to library 'C:/Users/biocbuild/bbs-3.4-bioc/R/library'
package 'rhdf5' successfully unpacked and MD5 sums checked