Package: rhdf5

Version: 1.7.0

Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD build rhdf5

RetCode: 1

Time: 29.9 seconds

Status: ERROR

PackageFile: None

* 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... no
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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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_ArraySubset':
hdf_dataset.c:339: warning: pointer targets in passing argument 3 of 'H5Sselect_hyperslab' differ in signedness
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 argument 4 of 'H5Sselect_elements' from incompatible pointer type
hdf_dataset.c: In function 'HDF_dataset_select_points':
hdf_dataset.c:483: warning: passing argument 4 of 'H5Sselect_elements' from incompatible pointer type
hdf_dataset.c: In function 'HDF_dataset_store':
hdf_dataset.c:526: warning: pointer targets in passing argument 2 of 'H5Screate_simple' differ in signedness
hdf_dataset.c: In function 'HDF_dataset_mat_load':
hdf_dataset.c:593: warning: pointer targets in passing argument 2 of 'H5Sget_simple_extent_dims' differ in signedness
hdf_dataset.c:596: warning: pointer targets in passing argument 2 of 'H5Screate_simple' differ in signedness
hdf_dataset.c:602: warning: pointer targets in passing argument 3 of 'setMatrixDims' differ in signedness
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -L/usr/local/include -I/usr/local/include    -fPIC  -g -O2 -Wall -c hdf_dataspace.c -o hdf_dataspace.o
hdf_dataspace.c: In function 'HDF_space_store':
hdf_dataspace.c:54: warning: pointer targets in passing argument 3 of 'H5Sselect_hyperslab' differ in signedness
hdf_dataspace.c: In function 'HDF_space_load':
hdf_dataspace.c:106: warning: pointer targets in passing argument 2 of 'H5Screate_simple' differ in signedness
hdf_dataspace.c:108: warning: pointer targets in passing argument 3 of 'H5Sselect_hyperslab' differ in signedness
hdf_dataspace.c:108: warning: pointer targets in passing argument 5 of 'H5Sselect_hyperslab' differ in signedness
hdf_dataspace.c: In function 'HDF_select_hyperslab':
hdf_dataspace.c:206: warning: pointer targets in passing argument 3 of 'H5Sselect_hyperslab' differ in signedness
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -L/usr/local/include -I/usr/local/include    -fPIC  -g -O2 -Wall -c hdf_plist.c -o hdf_plist.o
hdf_plist.c: In function 'HDF_plist_set_cache':
hdf_plist.c:30: warning: pointer targets in passing argument 3 of 'H5Pget_cache' differ in signedness
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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
hdf_subassign.c:208: warning: pointer targets in passing argument 3 of 'H5Sselect_hyperslab' differ in signedness
hdf_subassign.c:227: warning: pointer targets in passing argument 3 of 'H5Sselect_hyperslab' differ in signedness
hdf_subassign.c: In function 'HDF_ArraySubassign':
hdf_subassign.c:350: warning: pointer targets in passing argument 3 of 'H5Sselect_hyperslab' differ in signedness
hdf_subassign.c:361: warning: pointer targets in passing argument 3 of 'H5Sselect_hyperslab' differ in signedness
gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/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 -G -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.o hdf_group_apply.o hdf_initializer.o hdf_io.o hdf_plist.o hdf_register.o hdf_subassign.o hdf_util.o -L/usr/local/lib -lhdf5  -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR
** 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 in dyn.load(x, as.logical(local), as.logical(now)) : 
	unable to load shared library '/tmp/Rinst1693515124/rhdf5/libs/rhdf5.so':
  ld.so.1: R: fatal: relocation error: file /tmp/Rinst1693515124/rhdf5/libs/rhdf5.so: symbol vectorSubscript: referenced symbol not found

Error: processing vignette 'rhdf5.Rnw' failed with diagnostics:
 chunk 1 (label=loadlib) 
Error in library(rhdf5) : .First.lib failed for 'rhdf5'
Execution halted