rhdf5 2.6.0
Bernd Fischer
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/rhdf5 | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | [ OK ] | OK |
* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.6.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... NOTE
Found the following apparent object files/libraries:
src/libwin/i386/libhdf5ForBioC-7.dll src/libwin/i386/libsz-2.dll
src/libwin/x64/libhdf5ForBioC-7.dll src/libwin/x64/libsz-2.dll
Object files/libraries should not be included in a source package.
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘rhdf5’ can be installed ... [176s/199s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File ‘/Users/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck/rhdf5/libs/rhdf5.so’:
Found ‘_printf’, possibly from ‘printf’ (C)
Objects: ‘H5A.o’, ‘H5D.o’
Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
Objects: ‘H5A.o’, ‘H5D.o’, ‘H5S.o’
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
‘rhdf5.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
‘/Users/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck/00check.log’
for details.
* installing *source* package ‘rhdf5’ ...
** libs
cd hdf5source && \
gunzip -dc hdf5small.tgz | tar xf -;
mv hdf5source/hdf5 .
cd hdf5 && \
./configure CC="llvm-gcc-4.2 -arch x86_64 -std=gnu99" CPP="llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E" CXX="llvm-g++-4.2 -arch x86_64" CXXCPP="llvm-g++-4.2 -arch x86_64 -E" F77="gfortran-4.2 -arch x86_64" --build="" --with-pic
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checking shell variables initial values... done
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compiler 'llvm-gcc-4.2 -arch x86_64 -std=gnu99' is GNU gcc-4.2.1
No match to get fc_version_info for
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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: tools/misc/h5cc: No such file or directory
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.7
Configured on: Sat Apr 5 03:55:00 PDT 2014
Configured by: biocbuild@perceval.fhcrc.org
Configure mode: production
Host system: i386-apple-darwin10.8.0
Uname information: Darwin perceval.fhcrc.org 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3˜1/RELEASE_I386 i386
Byte sex: little-endian
Libraries:
Installation point: /Users/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/llvm-gcc-4.2 -arch x86_64 -std=gnu99 ( (GCC) 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00))
CFLAGS:
H5_CFLAGS: -std=c99 -pedantic -Wall -Wextra -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 -Wno-long-long -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wunreachable-code -Wendif-labels -Wdeclaration-after-statement -Wold-style-definition -Winvalid-pch -Wvariadic-macros -Wnonnull -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wc++-compat -Wvolatile-register-var -Wstrict-overflow -w -O3 -fomit-frame-pointer -finline-functions
AM_CFLAGS:
CPPFLAGS:
H5_CPPFLAGS: -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS:
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 all-am
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
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5CS.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Dmpio.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Fmpi.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDdirect.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpio.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpiposix.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5MFdbg.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Obogus.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Smpio.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5TS.o) has no symbols
/usr/bin/ranlib: file: .libs/libhdf5ForBioC.a(H5Zszip.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5CS.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Dmpio.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Fmpi.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5FDdirect.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpio.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5FDmpiposix.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5MFdbg.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Obogus.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Smpio.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5TS.o) has no symbols
ranlib: file: .libs/libhdf5ForBioC.a(H5Zszip.o) has no symbols
cp hdf5/src/.libs/libhdf5ForBioC.a .
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5A.c -o H5A.o
H5A.c: In function ‘H5Aread_helper_INTEGER’:
H5A.c:153: warning: unused variable ‘herr’
H5A.c: In function ‘H5Aread_helper_FLOAT’:
H5A.c:186: warning: unused variable ‘herr’
H5A.c: In function ‘H5Aread_helper_STRING’:
H5A.c:213: warning: unused variable ‘herr’
H5A.c:220: warning: unused variable ‘herr’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5D.c -o H5D.o
H5D.c: In function ‘H5Dread_helper_INTEGER’:
H5D.c:116: warning: unused variable ‘status’
H5D.c:113: warning: unused variable ‘status’
H5D.c:128: warning: unused variable ‘herr’
H5D.c:141: warning: unused variable ‘status’
H5D.c:138: warning: unused variable ‘status’
H5D.c:149: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_FLOAT’:
H5D.c:195: warning: unused variable ‘status’
H5D.c:192: warning: unused variable ‘status’
H5D.c:207: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_STRING’:
H5D.c:228: warning: unused variable ‘status’
H5D.c:225: warning: unused variable ‘status’
H5D.c:236: warning: unused variable ‘herr’
H5D.c:244: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_ENUM’:
H5D.c:276: warning: unused variable ‘status’
H5D.c:287: warning: unused variable ‘status’
H5D.c:284: warning: unused variable ‘status’
H5D.c:301: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:352: warning: unused variable ‘status’
H5D.c:349: warning: unused variable ‘status’
H5D.c:374: warning: unused variable ‘herr’
H5D.c: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:407: warning: unused variable ‘mem_type_id’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5F.c -o H5F.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5G.c -o H5G.o
H5G.c: In function ‘_H5Gget_info’:
H5G.c:66: warning: unused variable ‘herr’
H5G.c: In function ‘_H5Gget_info_by_name’:
H5G.c:113: warning: unused variable ‘herr’
H5G.c: In function ‘_H5Gget_info_by_idx’:
H5G.c:163: warning: unused variable ‘herr’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5I.c -o H5I.o
H5I.c: In function ‘_H5Iget_name’:
H5I.c:24: warning: passing argument 2 of ‘H5Iget_name’ from incompatible pointer type
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5L.c -o H5L.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5O.c -o H5O.o
H5O.c: In function ‘H5Oget_num_attrs’:
H5O.c:13: warning: unused variable ‘herr’
H5O.c: In function ‘_H5Oopen’:
H5O.c:56: warning: implicit declaration of function ‘addHandle’
H5O.c: In function ‘_H5Oclose’:
H5O.c:69: warning: implicit declaration of function ‘removeHandle’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5S.c -o H5S.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5T.c -o H5T.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c H5constants.c -o H5constants.o
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c HandleList.cpp -o HandleList.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c h5dump.c -o h5dump.o
h5dump.c: In function ‘opAddToLinfoTree’:
h5dump.c:60: warning: implicit declaration of function ‘H5Oget_num_attrs’
h5dump.c:89: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’
h5dump.c:91: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’
h5dump.c:99: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’
h5dump.c:101: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’
h5dump.c: In function ‘_h5dump’:
h5dump.c:289: warning: unused variable ‘herr’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c h5ls.c -o h5ls.o
h5ls.c: In function ‘opAddToLinfoList’:
h5ls.c:80: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’
h5ls.c:82: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’
h5ls.c:90: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 5 has type ‘long long unsigned int’
h5ls.c:92: warning: format ‘%lu’ expects type ‘long unsigned int’, but argument 6 has type ‘long long unsigned int’
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c printdatatype.c -o printdatatype.o
llvm-gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fPIC -mtune=core2 -g -O2 -Wall -c wrap.c -o wrap.o
llvm-g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -L/usr/local/lib -o rhdf5.so 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 libhdf5ForBioC.a -lz -lm -L. -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.13-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)