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BUILD BIN report for rhdf5 on merida1

This page was generated on 2019-04-16 11:56:13 -0400 (Tue, 16 Apr 2019).

Package 1305/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
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 UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK [ OK ]UNNEEDED, same version exists in internal repository

Summary

Package: rhdf5
Version: 2.26.2
Command: 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
StartedAt: 2019-04-16 04:38:42 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 04:39:23 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 40.1 seconds
RetCode: 0
Status:  OK 
PackageFile: rhdf5_2.26.2.tgz
PackageFileSize: 1.976 MiB

Command output

##############################################################################
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###
### Running command:
###
###   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
###
##############################################################################
##############################################################################


>>>>>>> 
>>>>>>> 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"