Package: rhdf5

Version: 2.22.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rhdf5_2.22.0.tar.gz

StartedAt: 2018-04-12 02:24:55 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:27:09 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 134.5 seconds

RetCode: 0

Status:  OK

CheckDir: rhdf5.Rcheck

Warnings: 0

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings rhdf5_2.22.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/rhdf5.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 ‘rhdf5/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rhdf5’ version ‘2.22.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is 32.4Mb
  sub-directories of 1Mb or more:
    include   1.6Mb
    lib      19.7Mb
    libs     10.6Mb
* 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 ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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/rhdf5.Rcheck/00check.log’
for details.

* installing *source* package ‘rhdf5’ ...
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... 
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checking for suffix of object files... o
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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.tgz ...
building the bundled hdf5 library...
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checking whether build environment is sane... yes
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checking for gawk... gawk
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checking shell variables initial values... done
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compiler 'gcc' is GNU gcc-5.4.0
CC_BASENAME is gcc.
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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: cannot access 'tools/misc/h5cc': No such file or directory
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF5 Version: 1.8.7
		  Configured on: Thu Apr 12 02:25:13 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: 
	     Installation point: /home/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/hdf5

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc
                         CFLAGS: -g -O2 -Wall
                      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: no
               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
+ for d in src
+ test src '!=' .
+ cd src
+ make lib
make[1]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
make[2]: Entering directory '/home/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
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LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo  |                  \
	sed -e 's/-L/:/g' -e 's/ //g'`"                               \
 ./H5make_libsettings > H5lib_settings.c  ||                               \
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    (rm -f H5lib_settings.c ; exit 1)
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  CC     H5Pdapl.lo
  CC     H5Pdcpl.lo
  CC     H5Pdeprec.lo
  CC     H5Pdxpl.lo
  CC     H5Pfapl.lo
  CC     H5Pfcpl.lo
  CC     H5Pfmpl.lo
  CC     H5Pgcpl.lo
  CC     H5Pint.lo
  CC     H5Plapl.lo
  CC     H5Plcpl.lo
  CC     H5Pocpl.lo
  CC     H5Pocpypl.lo
  CC     H5Pstrcpl.lo
  CC     H5Ptest.lo
  CC     H5R.lo
  CC     H5Rdeprec.lo
  CC     H5RC.lo
  CC     H5RS.lo
  CC     H5S.lo
  CC     H5Sall.lo
  CC     H5Sdbg.lo
  CC     H5Shyper.lo
  CC     H5Smpio.lo
  CC     H5Snone.lo
  CC     H5Spoint.lo
  CC     H5Sselect.lo
  CC     H5Stest.lo
  CC     H5SL.lo
  CC     H5SM.lo
  CC     H5SMbtree2.lo
  CC     H5SMcache.lo
  CC     H5SMmessage.lo
  CC     H5SMtest.lo
  CC     H5ST.lo
  CC     H5T.lo
  CC     H5Tarray.lo
  CC     H5Tbit.lo
  CC     H5Tcommit.lo
  CC     H5Tcompound.lo
  CC     H5Tconv.lo
  CC     H5Tcset.lo
  CC     H5Tdbg.lo
  CC     H5Tdeprec.lo
  CC     H5Tenum.lo
  CC     H5Tfields.lo
  CC     H5Tfixed.lo
  CC     H5Tfloat.lo
  CC     H5detect-H5detect.o
  CCLD   H5detect
LD_LIBRARY_PATH="$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-3.6-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
make[1]: Leaving directory '/home/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/00_pkg_src/rhdf5/src/hdf5/src'
configure:    HDF5_INCLUDE=hdf5/src
configure:    HDF5_LIB=hdf5/src/.libs/libhdf5ForBioC.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/biocbuild/bbs-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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-3.6-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 hdf5/src/.libs/libhdf5ForBioC.a -lz -lm -L. -L/home/biocbuild/bbs-3.6-bioc/R/lib -lR
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/include"
cp hdf5/src/*.h /home/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/include
mkdir -p "/home/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/lib"
cp hdf5/src/.libs/libhdf5ForBioC.a /home/biocbuild/bbs-3.6-bioc/meat/rhdf5.Rcheck/rhdf5/lib/libhdf5.a
installing to /home/biocbuild/bbs-3.6-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)

R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(rhdf5)
> 
> test_check("rhdf5")
HDF5-DIAG: Error detected in HDF5 (1.8.7) thread 0:
  #000: H5Dio.c line 266 in H5Dwrite(): can't write data
    major: Dataset
    minor: Write failed
  #001: H5Dio.c line 617 in H5D_write(): src and dest data spaces have different sizes
    major: Invalid arguments to routine
    minor: Bad value
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 139 SKIPPED: 1 FAILED: 0
> 
> proc.time()
   user  system elapsed 
  2.640   0.024   2.658 

name	user	system	elapsed
H5	0.000	0.000	0.001
H5A	0.116	0.000	0.118
H5D	0.108	0.000	0.107
H5F	0.004	0.000	0.006
H5G	0.008	0.000	0.005
H5I	0.072	0.000	0.072
H5IdComponent-class	0.000	0.000	0.001
H5L	0.008	0.000	0.005
H5O	0.012	0.000	0.012
H5P	0.004	0.000	0.002
H5P_DATASET_ACCESS	0.000	0.000	0.002
H5P_DATASET_CREATE	0.012	0.000	0.008
H5P_LINK_CREATE	0.004	0.000	0.004
H5S	0.032	0.000	0.032
H5T	0.000	0.000	0.001
h5const	0	0	0
h5createAttribute	0.012	0.000	0.012
h5createDataset	0.084	0.004	0.090
h5createFile	0.004	0.000	0.006
h5createGroup	0.008	0.000	0.007
h5errorHandling	0	0	0
h5listIdentifier	0.004	0.000	0.005
h5ls	0.020	0.000	0.021
h5save	0.032	0.000	0.032
h5set_extent	0.012	0.000	0.013
h5version	0.000	0.000	0.002
h5write	0.032	0.000	0.033
rhdf5	0.036	0.000	0.037