* checking for file 'rhdf5/DESCRIPTION' ... OK
* preparing 'rhdf5':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking whether 'INDEX' is up-to-date ... NO
* use '--force' to overwrite the existing 'INDEX'
* installing the package to re-build vignettes
* Installing *source* package 'rhdf5' ...
checking for gcc... gcc
checking for C compiler default output... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
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 ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for hdf5... yes
checking for H5Fopen in -lhdf5... yes
checking hdf5.h usability... yes
checking hdf5.h presence... yes
checking for hdf5.h... yes
checking hdf5 in /usr/local... ok
checking for hdf5 version >= 1.4... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf5.c -o hdf5.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_attribs.c -o hdf_attribs.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_convert.c -o hdf_convert.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_dataset.c -o hdf_dataset.o
hdf_dataset.c: In function `HDF_VectorSubset':
hdf_dataset.c:424: warning: implicit declaration of function `vectorSubscript'
hdf_dataset.c:424: warning: assignment makes pointer from integer without a cast
hdf_dataset.c:445: warning: passing arg 4 of `H5Sselect_elements' from incompatible pointer type
hdf_dataset.c: In function `HDF_dataset_select_points':
hdf_dataset.c:483: warning: passing arg 4 of `H5Sselect_elements' from incompatible pointer type
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_dataspace.c -o hdf_dataspace.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_datatype.c -o hdf_datatype.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_files.c -o hdf_files.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_group_apply.c -o hdf_group_apply.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_group.c -o hdf_group.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_initializer.c -o hdf_initializer.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_io.c -o hdf_io.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_plist.c -o hdf_plist.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_register.c -o hdf_register.o
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_subassign.c -o hdf_subassign.o
hdf_subassign.c: In function `HDF_VectorSubassign':
hdf_subassign.c:178: warning: implicit declaration of function `vectorSubscript'
hdf_subassign.c:178: warning: assignment makes pointer from integer without a cast
gcc -std=gnu99 -I/loc/biocbuild/2.0d/R/include -I/loc/biocbuild/2.0d/R/include -L/usr/local/include -I/usr/local/include -fpic -g -O2 -Wall -c hdf_util.c -o hdf_util.o
gcc -std=gnu99 -shared -L/usr/local/lib -o rhdf5.so hdf5.o hdf_attribs.o hdf_convert.o hdf_dataset.o hdf_dataspace.o hdf_datatype.o hdf_files.o hdf_group_apply.o hdf_group.o hdf_initializer.o hdf_io.o hdf_plist.o hdf_register.o hdf_subassign.o hdf_util.o -L/usr/local/lib -lhdf5
** R
** inst
** help
>>> Building/Updating help pages for package 'rhdf5'
Formats: text html latex example
Extract.hdf5 text html latex example
as.double.hdf5.dataset text html latex example
as.hdf5.dataset text html latex example
as.matrix.hdf5.dataset text html latex example
dim.hdf5 text html latex example
hdf5.apply text html latex example
hdf5.attributes text html latex example
hdf5.dataset text html latex example
hdf5.datatypes text html latex
hdf5.file text html latex example
hdf5.group text html latex example
hdf5.info text html latex example
hdf5.overview text html latex example
hdf5.plist.create text html latex example
hdf5.readcel text html latex example
is.finite text html latex example
is.matrix text html latex example
min.hdf5.dataset text html latex example
names.hdf5.file text html latex example
print.hdf5.dataspace text html latex example
space.hdf5.dataset text html latex example
swapmemory text html latex example
** building package indices ...
* DONE (rhdf5)
* creating vignettes ... ERROR
Error: chunk 1 (label=loadlib)
Error in library(rhdf5) : .First.lib failed for 'rhdf5'
Error in buildVignettes(dir = ".") : Error: chunk 1 (label=loadlib)
Error in library(rhdf5) : .First.lib failed for 'rhdf5'
Execution halted