Package: Rhdf5lib

Version: 1.0.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rhdf5lib_1.0.0.tar.gz

StartedAt: 2018-04-12 02:25:28 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:28:21 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 173.1 seconds

RetCode: 0

Status:  OK

CheckDir: Rhdf5lib.Rcheck

Warnings: 0

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###
### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings Rhdf5lib_1.0.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rhdf5lib/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘Rhdf5lib’ version ‘1.0.0’
* 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/winlib/i386/libhdf5.a src/winlib/i386/libhdf5_cpp.a
  src/winlib/i386/libszip.a src/winlib/x64/libhdf5.a
  src/winlib/x64/libhdf5_cpp.a src/winlib/x64/libszip.a
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 ‘Rhdf5lib’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 32.7Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib      20.1Mb
    libs     10.1Mb
* 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 ... OK
* 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 shell scripts ... 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 GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00check.log’
for details.

* installing *source* package ‘Rhdf5lib’ ...
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 g++... g++
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
untarring hdf5small_cxx_1.8.19.tar.gz ...
building the szip library...
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 make supports nested variables... 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
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checking for config linux-gnu... found
compiler 'gcc' is GNU gcc-5.4.0
checking for gcc... gcc
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checking command to parse /usr/bin/nm -B output from gcc object... ok
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checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/SZconfig.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making all in src
make[1]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/szip/src'
make  all-am
make[2]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/szip/src'
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -Wall -w -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -O2 -Wall -w -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c rice.c  -fPIC -DPIC -o rice.o
mv -f .deps/rice.Tpo .deps/rice.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -Wall -w -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c -o sz_api.lo sz_api.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -O2 -Wall -w -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c sz_api.c  -fPIC -DPIC -o sz_api.o
mv -f .deps/sz_api.Tpo .deps/sz_api.Plo
/bin/bash ../libtool  --tag=CC   --mode=compile gcc -DHAVE_CONFIG_H -I.     -O2 -Wall -w -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c
libtool: compile:  gcc -DHAVE_CONFIG_H -I. -O2 -Wall -w -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c encoding.c  -fPIC -DPIC -o encoding.o
mv -f .deps/encoding.Tpo .deps/encoding.Plo
/bin/bash ../libtool  --tag=CC   --mode=link gcc  -O2 -Wall -w -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -version-info 2:0:0  -o libsz.la -rpath /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/szip/szip/lib rice.lo sz_api.lo encoding.lo  -lm
libtool: link: ar cru .libs/libsz.a  rice.o sz_api.o encoding.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libsz.a
libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" )
make[2]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/szip'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/szip'
building the bundled hdf5 library...
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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 whether O_DIRECT is declared... yes
checking for posix_memalign... yes
checking if the direct I/O virtual file driver (VFD) is enabled... no
checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin
checking whether exception handling functions is checked during data conversions... yes
checking whether data accuracy is guaranteed during data conversions... yes
checking if the machine has window style path name... no
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 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 if alignment restrictions are strictly enforced... no
configure: creating ./config.lt
config.lt: creating libtool
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/libhdf5.settings
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating c++/Makefile
config.status: creating c++/src/Makefile
config.status: creating c++/src/h5c++
config.status: creating src/H5config.h
config.status: executing pubconf commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF5 Version: 1.8.19
		  Configured on: Thu Apr 12 02:25:52 EDT 2018
		  Configured by: biocbuild@malbec1
		 Configure mode: production
		    Host system: x86_64-unknown-linux-gnu
	      Uname information: Linux malbec1 4.4.0-119-generic #143-Ubuntu SMP Mon Apr 2 16:08:24 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
		       Byte sex: little-endian
		      Libraries: static
	     Installation point: /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/hdf5

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc
                         CFLAGS: -g -O2 -Wall -w -L../szip/src/.libs -I../szip/src
                      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 -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 -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-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -Wdate-time -Wopenmp-simd -Warray-bounds=2 -Wc99-c11-compat -O3 -fstdarg-opt
                      AM_CFLAGS: 
                       CPPFLAGS: 
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200112L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: 
               Shared C Library: no
               Static C Library: yes
  Statically Linked Executables: no
                        LDFLAGS: 
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
 	 	Extra libraries: -lsz -lz -ldl -lm 
 		       Archiver: ar
 		 	 Ranlib: ranlib
 	      Debugged Packages: 
		    API Tracing: no

Languages:
----------
                        Fortran: no

                            C++: yes
                   C++ Compiler: /usr/bin/g++
                      C++ Flags: 
                   H5 C++ Flags:  
                   AM C++ Flags: 
             Shared C++ Library: no
             Static C++ Library: yes

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),szip(encoder)
                            MPE: no
                     Direct VFD: no
                        dmalloc: no
Clear file buffers before write: yes
           Using memory checker: no
         Function Stack Tracing: no
      Strict File Format Checks: no
   Optimization Instrumentation: no
for d in src  . c++; do                                \
  if test $d != .; then                                        \
   (cd $d && make  lib) || exit 1;            \
  fi;                                                           \
done
make[1]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/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       H5Fint.lo
  CC       H5Faccum.lo
  CC       H5Fcwfs.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       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       H5HGquery.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       H5PL.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.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       H5VM.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     libhdf5.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[2]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/src'
make[1]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/c++'
make[2]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/c++'
make[2]: Nothing to be done for 'build-lib'.
make[2]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/c++'
+ cd src
+ make lib
make[2]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/c++/src'
make[3]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/c++/src'
  CXX      H5Exception.lo
  CXX      H5IdComponent.lo
  CXX      H5DataSpace.lo
  CXX      H5PropList.lo
  CXX      H5Library.lo
  CXX      H5FaccProp.lo
  CXX      H5FcreatProp.lo
  CXX      H5LaccProp.lo
  CXX      H5DxferProp.lo
  CXX      H5DcreatProp.lo
  CXX      H5Location.lo
  CXX      H5AbstractDs.lo
  CXX      H5Attribute.lo
  CXX      H5Object.lo
  CXX      H5OcreatProp.lo
  CXX      H5DataType.lo
  CXX      H5AtomType.lo
  CXX      H5PredType.lo
  CXX      H5EnumType.lo
  CXX      H5IntType.lo
  CXX      H5FloatType.lo
  CXX      H5StrType.lo
  CXX      H5ArrayType.lo
  CXX      H5VarLenType.lo
  CXX      H5CompType.lo
  CXX      H5DataSet.lo
  CXX      H5CommonFG.lo
  CXX      H5Group.lo
  CXX      H5File.lo
  CXXLD    libhdf5_cpp.la
ar: `u' modifier ignored since `D' is the default (see `U')
make[3]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/c++/src'
make[2]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/c++/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/00_pkg_src/Rhdf5lib/src/hdf5/c++'
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_CXX_INCLUDE=hdf5/c++/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure:    HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure:    SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/include"
cp hdf5/src/*.h /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/include
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/include/c++"
cp hdf5/c++/src/*.h /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/include/c++
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/lib/"
cp hdf5/src/.libs/libhdf5.a /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/lib/
cp hdf5/c++/src/.libs/libhdf5_cpp.a /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/lib/
cp hdf5/szip/src/.libs/libsz.a /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/lib/
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -Ihdf5/src  -fpic  -g -O2  -Wall -c Rhdf5lib.c -o Rhdf5lib.o
g++ -shared -L/home/biocbuild/bbs-3.6-bioc/R/lib -L/usr/local/lib -o Rhdf5lib.so Rhdf5lib.o hdf5/src/.libs/libhdf5.a hdf5/szip/src/.libs/libsz.a -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/include"
cp hdf5/src/*.h /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/include
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/include/c++"
cp hdf5/c++/src/*.h /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/include/c++
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/lib/"
cp hdf5/src/.libs/libhdf5.a /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/lib/
cp hdf5/c++/src/.libs/libhdf5_cpp.a /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/lib/
cp hdf5/szip/src/.libs/libsz.a /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/lib/
gcc -I/home/biocbuild/bbs-3.6-bioc/R/include -DNDEBUG   -I/usr/local/include  -Ihdf5/src  -fpic  -g -O2  -Wall -c Rhdf5lib.c -o Rhdf5lib.o
installing to /home/biocbuild/bbs-3.6-bioc/meat/Rhdf5lib.Rcheck/Rhdf5lib/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 (Rhdf5lib)

name	user	system	elapsed
getHdf5Version	0.000	0.000	0.001
pkgconfig	0.020	0.000	0.019