rhdf5 2.0.2
Bernd Fischer
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/rhdf5 | | Last Changed Rev: 65455 / Revision: 69725 | | Last Changed Date: 2012-04-26 11:31:59 -0700 (Thu, 26 Apr 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | OK | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | [ OK ] |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
install for i386
* installing *source* package 'rhdf5' ...
** libs
cp includeWin/i386/* includeWin/
cp libwin/i386/*.dll .
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-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:152:10: warning: unused variable 'herr' [-Wunused-variable]
H5A.c: In function 'H5Aread_helper_FLOAT':
H5A.c:185:10: warning: unused variable 'herr' [-Wunused-variable]
H5A.c: In function 'H5Aread_helper_STRING':
H5A.c:219:12: warning: unused variable 'herr' [-Wunused-variable]
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-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:108:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:105:12: warning: unused variable 'status' [-Wunused-variable]
H5D.c:120:10: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_FLOAT':
H5D.c:142:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:139:12: warning: unused variable 'status' [-Wunused-variable]
H5D.c:154:10: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_STRING':
H5D.c:184:9: warning: unused variable 'status' [-Wunused-variable]
H5D.c:181:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:189:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_COMPOUND':
H5D.c:203:9: warning: unused variable 'mem_type_id' [-Wunused-variable]
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=core2 -c H5F.c -o H5F.o
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-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]
H5G.c: In function '_H5Gget_info_by_name':
H5G.c:113:10: warning: unused variable 'herr' [-Wunused-variable]
H5G.c: In function '_H5Gget_info_by_idx':
H5G.c:163:10: warning: unused variable 'herr' [-Wunused-variable]
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-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:24:3: warning: passing argument 2 of 'H5Iget_name' from incompatible pointer type [enabled by default]
includeWin/H5Ipublic.h:85:16: note: expected 'char *' but argument is of type 'char (*)[(unsigned int)((int)st + 1)]'
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=core2 -c H5L.c -o H5L.o
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-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]
H5O.c: In function '_H5Oopen':
H5O.c:56:3: warning: implicit declaration of function 'addHandle' [-Wimplicit-function-declaration]
H5O.c: In function '_H5Oclose':
H5O.c:69:5: warning: implicit declaration of function 'removeHandle' [-Wimplicit-function-declaration]
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=core2 -c H5S.c -o H5S.o
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=core2 -c H5T.c -o H5T.o
gcc -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=core2 -c H5constants.c -o H5constants.o
g++ -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -mtune=core2 -c HandleList.cpp -o HandleList.o
HandleList.cpp: In function 'int removeHandle(hid_t)':
HandleList.cpp:175:1: warning: no return statement in function returning non-void [-Wreturn-type]
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-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:60:3: warning: implicit declaration of function 'H5Oget_num_attrs' [-Wimplicit-function-declaration]
h5dump.c:89:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5dump.c:91:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5dump.c:99:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5dump.c:101:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5dump.c: In function '_h5dump':
h5dump.c:289:10: warning: unused variable 'herr' [-Wunused-variable]
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-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:80:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5ls.c:82:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5ls.c:90:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5ls.c:92:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
gcc -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=core2 -c h5writeDataFrame.c -o h5writeDataFrame.o
h5writeDataFrame.c: In function '_h5writeDataFrame':
h5writeDataFrame.c:8:7: warning: unused variable 'level' [-Wunused-variable]
gcc -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-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]
printdatatype.c:19:16: warning: variable 'order_s' set but not used [-Wunused-but-set-variable]
gcc -I"E:/biocbld/BBS-2˜1.10-/R/include" -DNDEBUG -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O3 -Wall -std=gnu99 -mtune=core2 -c wrap.c -o wrap.o
C:\Rtools216\gcc-4.6.3\bin\nm.exe: 'libhdf5ForBioC': No such file
g++ -shared -s -static-libgcc -o rhdf5.dll tmp.def H5A.o H5D.o H5F.o H5G.o H5I.o H5L.o H5O.o H5S.o H5T.o H5constants.o HandleList.o h5dump.o h5ls.o h5writeDataFrame.o printdatatype.o wrap.o -llibhdf5ForBioC-7 -LE:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/libs/i386 -lzlib1bioc -llibsz-2 -lm -L. -LE:/biocbld/BBS-2~1.10-/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
'rhdf5.Rnw'
** testing if installed package can be loaded
install for x64
* installing *source* package 'rhdf5' ...
** libs
cp includeWin/x64/* includeWin/
cp libwin/x64/*.dll .
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-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:152:10: warning: unused variable 'herr' [-Wunused-variable]
H5A.c: In function 'H5Aread_helper_FLOAT':
H5A.c:185:10: warning: unused variable 'herr' [-Wunused-variable]
H5A.c: In function 'H5Aread_helper_STRING':
H5A.c:219:12: warning: unused variable 'herr' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-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:108:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:105:12: warning: unused variable 'status' [-Wunused-variable]
H5D.c:120:10: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_FLOAT':
H5D.c:142:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:139:12: warning: unused variable 'status' [-Wunused-variable]
H5D.c:154:10: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_STRING':
H5D.c:184:9: warning: unused variable 'status' [-Wunused-variable]
H5D.c:181:14: warning: unused variable 'status' [-Wunused-variable]
H5D.c:189:12: warning: unused variable 'herr' [-Wunused-variable]
H5D.c: In function 'H5Dread_helper_COMPOUND':
H5D.c:203:9: warning: unused variable 'mem_type_id' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=core2 -c H5F.c -o H5F.o
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-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]
H5G.c: In function '_H5Gget_info_by_name':
H5G.c:113:10: warning: unused variable 'herr' [-Wunused-variable]
H5G.c: In function '_H5Gget_info_by_idx':
H5G.c:163:10: warning: unused variable 'herr' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-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:24:3: warning: passing argument 2 of 'H5Iget_name' from incompatible pointer type [enabled by default]
includeWin/H5Ipublic.h:85:16: note: expected 'char *' but argument is of type 'char (*)[(long long unsigned int)(st + 1)]'
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=core2 -c H5L.c -o H5L.o
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-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]
H5O.c: In function '_H5Oopen':
H5O.c:56:3: warning: implicit declaration of function 'addHandle' [-Wimplicit-function-declaration]
H5O.c: In function '_H5Oclose':
H5O.c:69:5: warning: implicit declaration of function 'removeHandle' [-Wimplicit-function-declaration]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=core2 -c H5S.c -o H5S.o
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=core2 -c H5T.c -o H5T.o
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=core2 -c H5constants.c -o H5constants.o
g++ -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -mtune=core2 -c HandleList.cpp -o HandleList.o
HandleList.cpp: In function 'int removeHandle(hid_t)':
HandleList.cpp:175:1: warning: no return statement in function returning non-void [-Wreturn-type]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-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:60:3: warning: implicit declaration of function 'H5Oget_num_attrs' [-Wimplicit-function-declaration]
h5dump.c:89:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5dump.c:91:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5dump.c:99:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5dump.c:101:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5dump.c: In function '_h5dump':
h5dump.c:289:10: warning: unused variable 'herr' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-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:80:7: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5ls.c:82:8: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
h5ls.c:90:2: warning: format '%lu' expects argument of type 'long unsigned int', but argument 3 has type 'hsize_t' [-Wformat]
h5ls.c:92:4: warning: format '%lu' expects argument of type 'long unsigned int', but argument 4 has type 'hsize_t' [-Wformat]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=core2 -c h5writeDataFrame.c -o h5writeDataFrame.o
h5writeDataFrame.c: In function '_h5writeDataFrame':
h5writeDataFrame.c:8:7: warning: unused variable 'level' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-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]
printdatatype.c:19:16: warning: variable 'order_s' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-2~1.10-/R/include" -DNDEBUG -I"d:/RCompile/CRANpkg/extralibs64/local/include" -I"E:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/include" -IincludeWin -DWINDOWS -O2 -Wall -std=gnu99 -mtune=core2 -c wrap.c -o wrap.o
C:\Rtools216\gcc-4.6.3\bin\nm.exe: 'libhdf5ForBioC': No such file
g++ -m64 -shared -s -static-libgcc -o rhdf5.dll tmp.def H5A.o H5D.o H5F.o H5G.o H5I.o H5L.o H5O.o H5S.o H5T.o H5constants.o HandleList.o h5dump.o h5ls.o h5writeDataFrame.o printdatatype.o wrap.o -llibhdf5ForBioC-7 -LE:/biocbld/bbs-2.10-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -llibsz-2 -lm -L. -Ld:/RCompile/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LE:/biocbld/BBS-2~1.10-/R/bin/x64 -lR
installing to E:/biocbld/bbs-2.10-bioc/meat/rhdf5.buildbin-libdir/rhdf5/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rhdf5' as rhdf5_2.0.2.zip
* DONE (rhdf5)