* installing *source* package ‘rhdf5’ ...
** libs
cd hdf5source && \
gunzip -dc hdf5small.tgz | tar xf -;
rm -rf hdf5
mv hdf5source/hdf5 .
cd hdf5 && \
./configure CC="gcc" CPP="gcc -E" CXX="g++ " CXXCPP="g++ -E" F77="f95" --build="" --with-pic
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config unknown-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-linux-gnu... no
checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'gcc' is GNU gcc-5.4.0
CC_BASENAME is gcc.
checking for config ./config/site-specific/host-malbec2... no
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for style of include used by make... GNU
checking dependency style of gcc... gcc3
checking if unsupported combinations of configure options are allowed... no
checking if Fortran interface enabled... no
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking dependency style of g++ ... gcc3
checking how to run the C++ preprocessor... g++ -E
checking if c++ interface enabled... no
checking for perl... perl
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
checking for tr... /usr/bin/tr
checking if srcdir= and time commands work together... yes
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for fgrep... /bin/grep -F
checking for ld used by gcc... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking whether the shell understands some XSI constructs... yes
checking whether the shell understands "+="... yes
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... dlltool
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for mt... mt
checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... yes
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... yes
checking if we should install only statically linked executables... no
checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes
checking make... checking how make searches directories... VPATH=DIR1 DIR2 ...
checking whether make will build with undefined variables... yes
checking for production mode... production
checking for ceil in -lm... yes
checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking for difftime... yes
checking for gettimeofday... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
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checking sys/time.h usability... yes
checking sys/time.h presence... yes
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checking for unistd.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking for sys/stat.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/types.h... (cached) yes
checking stddef.h usability... yes
checking stddef.h presence... yes
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checking setjmp.h usability... yes
checking setjmp.h presence... yes
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checking features.h usability... yes
checking features.h presence... yes
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checking for stdint.h... (cached) yes
checking io.h usability... no
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checking winsock.h usability... no
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checking for winsock.h... no
checking sys/timeb.h usability... yes
checking sys/timeb.h presence... yes
checking for sys/timeb.h... yes
checking if libtool needs -no-undefined flag to build shared libraries... no
checking if configure should try to set up large file support... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking if large (64-bit) files are supported on this system.... yes
checking for lseek64... yes
checking for fseeko64... yes
checking for ftello64... yes
checking for ftruncate64... yes
checking for fseeko... yes
checking for ftello... yes
checking for stat64... yes
checking for fstat64... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking whether byte ordering is bigendian... no
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of unsigned... 4
checking size of long... 8
checking size of long long... 8
checking size of __int64... 0
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of int8_t... 1
checking size of uint8_t... 1
checking size of int_least8_t... 1
checking size of uint_least8_t... 1
checking size of int_fast8_t... 1
checking size of uint_fast8_t... 1
checking size of int16_t... 2
checking size of uint16_t... 2
checking size of int_least16_t... 2
checking size of uint_least16_t... 2
checking size of int_fast16_t... 8
checking size of uint_fast16_t... 8
checking size of int32_t... 4
checking size of uint32_t... 4
checking size of int_least32_t... 4
checking size of uint_least32_t... 4
checking size of int_fast32_t... 8
checking size of uint_fast32_t... 8
checking size of int64_t... 8
checking size of uint64_t... 8
checking size of int_least64_t... 8
checking size of uint_least64_t... 8
checking size of int_fast64_t... 8
checking size of uint_fast64_t... 8
checking size of size_t... 8
checking size of ssize_t... 8
checking size of ptrdiff_t... 8
checking size of off_t... 8
checking size of off64_t... 8
checking if dev_t is scalar... yes
checking for dmalloc library... suppressed
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for compress2 in -lz... yes
checking for compress2... yes
checking for szlib... suppressed
checking for pthread... suppressed
checking for thread safe support... no
checking for tm_gmtoff in struct tm... yes
checking for __tm_gmtoff in struct tm... no
checking for global timezone variable... yes
checking whether struct tm is in sys/time.h or time.h... time.h
checking for struct tm.tm_zone... yes
checking for struct timezone... yes
checking whether gettimeofday() gives timezone... yes
checking for st_blocks in struct stat... yes
checking for _getvideoconfig... no
checking for gettextinfo... no
checking for GetConsoleScreenBufferInfo... no
checking for _scrsize... no
checking for ioctl... yes
checking for struct videoconfig... no
checking for struct text_info... no
checking for TIOCGWINSZ... yes
checking for TIOCGETD... yes
checking for alarm... yes
checking for BSDgettimeofday... no
checking for fork... yes
checking for frexpf... yes
checking for frexpl... yes
checking for gethostname... yes
checking for getpwuid... yes
checking for getrusage... yes
checking for lstat... yes
checking for rand_r... yes
checking for random... yes
checking for setsysinfo... no
checking for signal... yes
checking for longjmp... yes
checking for setjmp... yes
checking for siglongjmp... yes
checking for sigsetjmp... no
checking for sigprocmask... yes
checking for snprintf... yes
checking for srandom... yes
checking for strdup... yes
checking for symlink... yes
checking for system... yes
checking for tmpfile... yes
checking for vasprintf... yes
checking for waitpid... yes
checking for vsnprintf... yes
checking if vsnprintf returns correct value... yes
checking if lone colon can be used as an argument... yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for __attribute__ extension... yes
checking for __func__ extension... yes
checking for __FUNCTION__ extension... yes
checking for C99 designated initialization support... yes
checking how to print long long... %ld and %lu
checking Threads support system scope... yes
checking for gpfs... suppressed
checking for debug flags... none
checking whether function stack tracking is enabled... no
checking whether metadata trace file code is enabled... no
checking for API tracing... no
checking for instrumented library... no
checking whether to clear file buffers... yes
checking whether a memory checking tool will be used... no
checking for parallel support files... skipped
checking for I/O filters... all (shuffle,fletcher32,nbit,scaleoffset)
checking for Default Virtual File Driver definition... yes
checking for Direct Virtual File Driver support... no
checking whether exception handling functions is checked during data conversions... yes
checking whether data accuracy is guaranteed during data conversions... yes
checking if converting denormalized floating-point values is possible... yes
checking if converting floating-point values to long long is not working... false
checking if the machine has window style path name... no
checking if converting from long double to integers is accurate... yes
checking if converting from long double to integers works... yes
checking if accurately converting from integers to long double... yes
checking if accurately converting unsigned long to float values... yes
checking if accurately converting unsigned long long to floating-point values... yes
checking if accurately roundup converting floating-point to unsigned long long values... yes
checking if right maximum converting floating-point to unsigned long long values... no
checking if correctly converting long double to unsigned int values... yes
checking if compiling unsigned long long to floating-point typecasts work... yes
checking if compiling long long to floating-point typecasts work... yes
checking if converting unsigned long long to long double with precision... yes
checking if overflows normally converting floating-point to integer values... yes
checking if using special algorithm to convert long double to (unsigned) long values... no
checking if using special algorithm to convert (unsigned) long to long double values... no
checking if correctly converting long double to (unsigned) long long values... yes
checking if correctly converting (unsigned) long long to long double values... yes
checking if bad code for log2 routine is generated... no
checking if high level library is enabled... yes
checking additional programs should be built... no
checking if deprecated public symbols are available... yes
checking which version of public symbols to use by default... v18
checking Whether to perform strict file format checks... no
checking Whether to have library information embedded in the executables... yes
checking Whether to enable the h5dump packed bits feature... yes
checking if alignment restrictions are strictly enforced... no
configure: creating ./config.status
configure: creating ./config.lt
config.lt: creating libtool
config.status: creating src/libhdf5.settings
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/H5config.h
config.status: executing default-1 commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
chmod: cannot access 'tools/misc/h5cc': No such file or directory
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.7
Configured on: Wed Aug 16 01:50:37 EDT 2017
Configured by: biocbuild@malbec2
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux malbec2 4.4.0-83-generic #106-Ubuntu SMP Mon Jun 26 17:54:43 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /home/biocbuild/bbs-3.5-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc
CFLAGS:
H5_CFLAGS: -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -w -O -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -D_POSIX_SOURCE -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS:
H5_LDFLAGS:
AM_LDFLAGS:
Extra libraries: -lz -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: no
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib)
I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
MPE: no
Direct VFD: no
dmalloc: no
Clear file buffers before write: yes
Using memory checker: no
Function Stack Tracing: no
GPFS: no
Strict File Format Checks: no
Optimization Instrumentation: no
Large File Support (LFS): yes
H5dump Packed Bits: yes
cd hdf5/src && \
make
make[1]: Entering directory '/home/biocbuild/bbs-3.5-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
make all-am
make[2]: Entering directory '/home/biocbuild/bbs-3.5-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
CC H5.lo
CC H5checksum.lo
CC H5dbg.lo
CC H5system.lo
CC H5timer.lo
CC H5trace.lo
CC H5A.lo
CC H5Abtree2.lo
CC H5Adense.lo
CC H5Adeprec.lo
CC H5Aint.lo
CC H5Atest.lo
CC H5AC.lo
CC H5B.lo
CC H5Bcache.lo
CC H5Bdbg.lo
CC H5B2.lo
CC H5B2cache.lo
CC H5B2dbg.lo
CC H5B2hdr.lo
CC H5B2int.lo
CC H5B2stat.lo
CC H5B2test.lo
CC H5C.lo
CC H5CS.lo
CC H5D.lo
CC H5Dbtree.lo
CC H5Dchunk.lo
CC H5Dcompact.lo
CC H5Dcontig.lo
CC H5Ddbg.lo
CC H5Ddeprec.lo
CC H5Defl.lo
CC H5Dfill.lo
CC H5Dint.lo
CC H5Dio.lo
CC H5Dlayout.lo
CC H5Dmpio.lo
CC H5Doh.lo
CC H5Dscatgath.lo
CC H5Dselect.lo
CC H5Dtest.lo
CC H5E.lo
CC H5Edeprec.lo
CC H5Eint.lo
CC H5F.lo
CC H5Faccum.lo
CC H5Fdbg.lo
CC H5Fefc.lo
CC H5Ffake.lo
CC H5Fio.lo
CC H5Fmount.lo
CC H5Fmpi.lo
CC H5Fquery.lo
CC H5Fsfile.lo
CC H5Fsuper.lo
CC H5Fsuper_cache.lo
CC H5Ftest.lo
CC H5FD.lo
CC H5FDcore.lo
CC H5FDdirect.lo
CC H5FDfamily.lo
CC H5FDint.lo
CC H5FDlog.lo
CC H5FDmpi.lo
CC H5FDmpio.lo
CC H5FDmpiposix.lo
CC H5FDmulti.lo
CC H5FDsec2.lo
CC H5FDspace.lo
CC H5FDstdio.lo
CC H5FL.lo
CC H5FO.lo
CC H5FS.lo
CC H5FScache.lo
CC H5FSdbg.lo
CC H5FSsection.lo
CC H5FSstat.lo
CC H5FStest.lo
CC H5G.lo
CC H5Gbtree2.lo
CC H5Gcache.lo
CC H5Gcompact.lo
CC H5Gdense.lo
CC H5Gdeprec.lo
CC H5Gent.lo
CC H5Gint.lo
CC H5Glink.lo
CC H5Gloc.lo
CC H5Gname.lo
CC H5Gnode.lo
CC H5Gobj.lo
CC H5Goh.lo
CC H5Groot.lo
CC H5Gstab.lo
CC H5Gtest.lo
CC H5Gtraverse.lo
CC H5HF.lo
CC H5HFbtree2.lo
CC H5HFcache.lo
CC H5HFdbg.lo
CC H5HFdblock.lo
CC H5HFdtable.lo
CC H5HFhdr.lo
CC H5HFhuge.lo
CC H5HFiblock.lo
CC H5HFiter.lo
CC H5HFman.lo
CC H5HFsection.lo
CC H5HFspace.lo
CC H5HFstat.lo
CC H5HFtest.lo
CC H5HFtiny.lo
CC H5HG.lo
CC H5HGcache.lo
CC H5HGdbg.lo
CC H5HL.lo
CC H5HLcache.lo
CC H5HLdbg.lo
CC H5HLint.lo
CC H5HP.lo
CC H5I.lo
CC H5Itest.lo
CC H5L.lo
CC H5Lexternal.lo
CC H5make_libsettings.o
CCLD H5make_libsettings
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5make_libsettings > H5lib_settings.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5lib_settings.c ; exit 1)
CC H5lib_settings.lo
CC H5MF.lo
CC H5MFaggr.lo
CC H5MFdbg.lo
CC H5MFsection.lo
CC H5MM.lo
CC H5MP.lo
CC H5MPtest.lo
CC H5O.lo
CC H5Oainfo.lo
CC H5Oalloc.lo
CC H5Oattr.lo
CC H5Oattribute.lo
CC H5Obogus.lo
CC H5Obtreek.lo
CC H5Ocache.lo
CC H5Ochunk.lo
CC H5Ocont.lo
CC H5Ocopy.lo
CC H5Odbg.lo
CC H5Odrvinfo.lo
CC H5Odtype.lo
CC H5Oefl.lo
CC H5Ofill.lo
CC H5Oginfo.lo
CC H5Olayout.lo
CC H5Olinfo.lo
CC H5Olink.lo
CC H5Omessage.lo
CC H5Omtime.lo
CC H5Oname.lo
CC H5Onull.lo
CC H5Opline.lo
CC H5Orefcount.lo
CC H5Osdspace.lo
CC H5Oshared.lo
CC H5Ostab.lo
CC H5Oshmesg.lo
CC H5Otest.lo
CC H5Ounknown.lo
CC H5P.lo
CC H5Pacpl.lo
CC H5Pdapl.lo
CC H5Pdcpl.lo
CC H5Pdeprec.lo
CC H5Pdxpl.lo
CC H5Pfapl.lo
CC H5Pfcpl.lo
CC H5Pfmpl.lo
CC H5Pgcpl.lo
CC H5Pint.lo
CC H5Plapl.lo
CC H5Plcpl.lo
CC H5Pocpl.lo
CC H5Pocpypl.lo
CC H5Pstrcpl.lo
CC H5Ptest.lo
CC H5R.lo
CC H5Rdeprec.lo
CC H5RC.lo
CC H5RS.lo
CC H5S.lo
CC H5Sall.lo
CC H5Sdbg.lo
CC H5Shyper.lo
CC H5Smpio.lo
CC H5Snone.lo
CC H5Spoint.lo
CC H5Sselect.lo
CC H5Stest.lo
CC H5SL.lo
CC H5SM.lo
CC H5SMbtree2.lo
CC H5SMcache.lo
CC H5SMmessage.lo
CC H5SMtest.lo
CC H5ST.lo
CC H5T.lo
CC H5Tarray.lo
CC H5Tbit.lo
CC H5Tcommit.lo
CC H5Tcompound.lo
CC H5Tconv.lo
CC H5Tcset.lo
CC H5Tdbg.lo
CC H5Tdeprec.lo
CC H5Tenum.lo
CC H5Tfields.lo
CC H5Tfixed.lo
CC H5Tfloat.lo
CC H5detect-H5detect.o
CCLD H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5detect > H5Tinit.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5Tinit.c ; exit 1)
CC H5Tinit.lo
CC H5Tnative.lo
CC H5Toffset.lo
CC H5Toh.lo
CC H5Topaque.lo
CC H5Torder.lo
CC H5Tpad.lo
CC H5Tprecis.lo
CC H5Tstrpad.lo
CC H5Tvisit.lo
CC H5Tvlen.lo
CC H5TS.lo
CC H5V.lo
CC H5WB.lo
CC H5Z.lo
CC H5Zdeflate.lo
CC H5Zfletcher32.lo
CC H5Znbit.lo
CC H5Zshuffle.lo
CC H5Zszip.lo
CC H5Zscaleoffset.lo
CC H5Ztrans.lo
CCLD libhdf5ForBioC.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/home/biocbuild/bbs-3.5-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.5-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
cp hdf5/src/.libs/libhdf5ForBioC.a .
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5.c -o H5.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -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 );
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -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));
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5E.c -o H5E.o
In file included from /home/biocbuild/bbs-3.5-bioc/R/include/R.h:86:0,
from H5E.h:4,
from H5E.c:1:
H5E.c: In function ‘custom_print_cb’:
/home/biocbuild/bbs-3.5-bioc/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’:
/home/biocbuild/bbs-3.5-bioc/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);
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -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 [-Wincompatible-pointer-types]
size = H5Fget_name( obj_id, &name, size+1);
^
In file included from hdf5/src/hdf5.h:29:0,
from myhdf5.h:7,
from H5F.h:8,
from H5F.c:1:
hdf5/src/H5Fpublic.h:174:16: note: expected ‘char *’ but argument is of type ‘char (*)[(sizetype)(size + 1l)]’
H5_DLL ssize_t H5Fget_name(hid_t obj_id, char *name, size_t size);
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -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 );
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -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 [-Wincompatible-pointer-types]
H5Iget_name( obj_id, &name, st+1 );
^
In file included from hdf5/src/H5Apublic.h:23:0,
from hdf5/src/hdf5.h:25,
from myhdf5.h:7,
from H5I.h:8,
from H5I.c:1:
hdf5/src/H5Ipublic.h:85:16: note: expected ‘char *’ but argument is of type ‘char (*)[(sizetype)(st + 1l)]’
H5_DLL ssize_t H5Iget_name(hid_t id, char *name/*out*/, size_t size);
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5L.c -o H5L.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -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);
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -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];
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5S.c -o H5S.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5T.c -o H5T.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5constants.c -o H5constants.o
g++ -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c HandleListWrap.c -o HandleListWrap.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c h5dump.c -o h5dump.o
h5dump.c: In function ‘opAddToLinfoTree’:
h5dump.c:85:27: warning: implicit declaration of function ‘H5Oget_num_attrs’ [-Wimplicit-function-declaration]
newElement->num_attrs = H5Oget_num_attrs(oid);
^
h5dump.c:114:20: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
sprintf(tmp, "%lu", size[newElement->rank-1]);
^
h5dump.c:116:21: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, size[i]);
^
h5dump.c:124:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
sprintf(tmp, "%lu", maxsize[newElement->rank-1]);
^
h5dump.c:126:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘hsize_t {aka long long unsigned int}’ [-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 );
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c h5ls.c -o h5ls.o
h5ls.c: In function ‘opAddToLinfoList’:
h5ls.c:99:15: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
sprintf(tmp, "%lu", size[newElement->rank-1]);
^
h5ls.c:101:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, size[i]);
^
h5ls.c:109:17: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 3 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
sprintf(tmp, "%lu", maxsize[newElement->rank-1]);
^
h5ls.c:111:19: warning: format ‘%lu’ expects argument of type ‘long unsigned int’, but argument 4 has type ‘hsize_t {aka long long unsigned int}’ [-Wformat=]
sprintf(tmp, "%s x %lu", tmp, maxsize[i]);
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -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 */
^
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c wrap.c -o wrap.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/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 h5writeDataFrame.o printdatatype.o wrap.o libhdf5ForBioC.a -lz -lm -L. -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/meat/rhdf5.Rcheck/rhdf5/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rhdf5)
