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 ‘/home/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [157s/190s] 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 ‘/home/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck/rhdf5/libs/rhdf5.so’:
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 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 ... [1s/1s] 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
‘/home/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="gcc -std=gnu99" CPP="gcc -std=gnu99 -E" CXX="g++" CXXCPP="g++ -E" F77="gfortran" --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
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checking for config linux-gnu... found
compiler 'gcc -std=gnu99' is GNU gcc-4.6.3
CC_BASENAME is gcc.
checking for config ./config/site-specific/host-zin1... no
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
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checking for gcc -std=gnu99 option to accept ISO C89... none needed
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checking dependency style of g++... gcc3
checking how to run the C++ preprocessor... g++ -E
checking if c++ interface enabled... no
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checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
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checking for ld used by gcc -std=gnu99... /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... 3458764513820540925
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 -std=gnu99 object... ok
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checking if mt is a manifest tool... no
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for ANSI C header files... yes
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checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 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
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checking make... checking how make searches directories... VPATH=DIR1 DIR2 ...
checking whether make will build with undefined variables... yes
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checking for ceil in -lm... yes
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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
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checking if correctly converting long double to (unsigned) long long values... yes
checking if correctly converting (unsigned) long long to long double values... yes
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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: Sat Apr 5 03:33:19 PDT 2014
Configured by: biocbuild@zin1
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux zin1 3.2.0-38-generic #61-Ubuntu SMP Tue Feb 19 12:18:21 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Libraries:
Installation point: /home/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/hdf5
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /usr/bin/gcc -std=gnu99
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 -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 -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-aliasing -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -w -O3 -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-2.13-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
make all-am
make[2]: Entering directory `/home/biocbuild/bbs-2.13-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)
unable to calculate alignment for long double
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
make[2]: Leaving directory `/home/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
make[1]: Leaving directory `/home/biocbuild/bbs-2.13-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
cp hdf5/src/.libs/libhdf5ForBioC.a .
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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]
H5A.c: In function ‘H5Aread_helper_FLOAT’:
H5A.c:186:10: warning: unused variable ‘herr’ [-Wunused-variable]
H5A.c: In function ‘H5Aread_helper_STRING’:
H5A.c:213:12: warning: unused variable ‘herr’ [-Wunused-variable]
H5A.c:220:12: warning: unused variable ‘herr’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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:116:9: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:113:14: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:128:12: warning: unused variable ‘herr’ [-Wunused-variable]
H5D.c:141:9: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:138:14: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:149:12: warning: unused variable ‘herr’ [-Wunused-variable]
H5D.c: In function ‘H5Dread_helper_FLOAT’:
H5D.c:195:14: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:192:12: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:207:10: warning: unused variable ‘herr’ [-Wunused-variable]
H5D.c: In function ‘H5Dread_helper_STRING’:
H5D.c:228:14: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:225:12: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:236:12: warning: unused variable ‘herr’ [-Wunused-variable]
H5D.c:244:12: warning: unused variable ‘herr’ [-Wunused-variable]
H5D.c: In function ‘H5Dread_helper_ENUM’:
H5D.c:276:14: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:287:9: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:284:14: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:301:12: warning: unused variable ‘herr’ [-Wunused-variable]
H5D.c: In function ‘H5Dread_helper_ARRAY’:
H5D.c:352:13: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:349:14: warning: unused variable ‘status’ [-Wunused-variable]
H5D.c:374:12: warning: unused variable ‘herr’ [-Wunused-variable]
H5D.c: In function ‘H5Dread_helper_COMPOUND’:
H5D.c:407:9: warning: unused variable ‘mem_type_id’ [-Wunused-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5F.c -o H5F.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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]
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 -std=gnu99 -I/home/biocbuild/bbs-2.13-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:24:3: warning: passing argument 2 of ‘H5Iget_name’ from incompatible pointer type [enabled by default]
hdf5/src/H5Ipublic.h:85:16: note: expected ‘char *’ but argument is of type ‘char (*)[(long unsigned int)(st + 1)]’
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5L.c -o H5L.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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]
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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5S.c -o H5S.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c H5T.c -o H5T.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c HandleList.cpp -o HandleList.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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: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 -std=gnu99 -I/home/biocbuild/bbs-2.13-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: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 -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c h5writeDataFrame.c -o h5writeDataFrame.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-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]
printdatatype.c:19:16: warning: variable ‘order_s’ set but not used [-Wunused-but-set-variable]
gcc -std=gnu99 -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG -I/usr/local/include -Ihdf5/src -fpic -g -O2 -Wall -c wrap.c -o wrap.o
g++ -shared -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. -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/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)