[BioC] Help needed to install Rhdf5

[ying chen]

I am new to R and Bioconductor and I really appreciate your help.

I downloaded 5-1.6.0-linux-gcc3.2.2.tar.gz from HDF5 site.  I decompressed 
the tarball and moved it to /usr/lib, then I cd to /bin and typed 
./h5redeploy.  It seemed that everything went well as I got no error 
message.  But wheh I started R and tried to install Rhdf5, I got the 
following error message:

[1] "Attempting to download rhdf5 from
http://www.bioconductor.org/repository/release1.2/package/Sou
rce"
[1] "Download complete."
[1] "Installing rhdf5"
* 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 executable suffix...
checking for object suffix... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking how to run the C preprocessor... gcc -E
checking for hdf5... yes
checking for H5Fopen in -lhdf5... yes
checking for hdf5.h... yes
checking hdf5 in /usr/local... ok
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf5.c -o hdf5.o
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_attribs.c -o
hdf_attribs.o
hdf_attribs.c: In function `HDF_attr_set':
hdf_attribs.c:25: warning: `attr' might be used uninitialized in this
function
hdf_attribs.c: In function `getattrbyindex':
hdf_attribs.c:166: warning: `ans' might be used uninitialized in this
function
hdf_attribs.c: In function `HDF_getRtype':
hdf_attribs.c:308: warning: `attr' might be used uninitialized in this
function
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_convert.c -o
hdf_convert.o
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_dataset.c -o
hdf_dataset.o
hdf_dataset.c: In function `HDF_dataset_select_points':
hdf_dataset.c:471: warning: assignment from incompatible pointer type
hdf_dataset.c: In function `HDF_dataset_range':
hdf_dataset.c:1013: warning: `ans' might be used uninitialized in this
function
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_dataspace.c -o
hdf_dataspace.o
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_datatype.c -o
hdf_datatype.o
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_files.c -o hdf_files.o
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_group_apply.c -o
hdf_group_apply.o
hdf_group_apply.c: In function `HDF_masked_count':
hdf_group_apply.c:39: warning: enumeration value `H5G_UNKNOWN' not handled
in switch
hdf_group_apply.c:39: warning: enumeration value `H5G_RESERVED_4' not
handled in switch
hdf_group_apply.c:39: warning: enumeration value `H5G_RESERVED_5' not
handled in switch
hdf_group_apply.c:39: warning: enumeration value `H5G_RESERVED_6' not
handled in switch
hdf_group_apply.c:39: warning: enumeration value `H5G_RESERVED_7' not
handled in switch
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_group.c -o hdf_group.o
hdf_group.c: In function `HDF_print_iterator':
hdf_group.c:38: warning: enumeration value `H5G_UNKNOWN' not handled in
switch
hdf_group.c:38: warning: enumeration value `H5G_LINK' not handled in switch
hdf_group.c:38: warning: enumeration value `H5G_TYPE' not handled in switch
hdf_group.c:38: warning: enumeration value `H5G_RESERVED_4' not handled in
switch
hdf_group.c:38: warning: enumeration value `H5G_RESERVED_5' not handled in
switch
hdf_group.c:38: warning: enumeration value `H5G_RESERVED_6' not handled in
switch
hdf_group.c:38: warning: enumeration value `H5G_RESERVED_7' not handled in
switch
gcc -I/usr/lib/R/include -L/usr/local/include -I/usr/local/include
-D__NO_MATH_INLINES -mieee-fp -Wa
ll -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c hdf_initializer.c -o
hdf_initializer.o
hdf_initializer.c: In function `H5finalize':
hdf_initializer.c:66: `H5I_TEMPLATE_0' undeclared (first use in this
function)
hdf_initializer.c:66: (Each undeclared identifier is reported only once
hdf_initializer.c:66: for each function it appears in.)
hdf_initializer.c:67: `H5I_TEMPLATE_1' undeclared (first use in this
function)
hdf_initializer.c:68: `H5I_TEMPLATE_2' undeclared (first use in this
function)
hdf_initializer.c:69: `H5I_TEMPLATE_3' undeclared (first use in this
function)
hdf_initializer.c:70: `H5I_TEMPLATE_4' undeclared (first use in this
function)
hdf_initializer.c:71: `H5I_TEMPLATE_5' undeclared (first use in this
function)
hdf_initializer.c:72: `H5I_TEMPLATE_6' undeclared (first use in this
function)
hdf_initializer.c:73: `H5I_TEMPLATE_7' undeclared (first use in this
function)
hdf_initializer.c:80: `H5I_TEMPLATE_MAX' undeclared (first use in this
function)
make: *** [hdf_initializer.o] Error 1
ERROR: compilation failed for package 'rhdf5'
>From URL:  http://www.bioconductor.org/repository/release1.2/package/Source
        rhdf5 version 1.0.1

Packages that were not updated:
        graph
        hexbin
        DynDoc
        Ruuid
        Biobase
        tkWidgets
        widgetTools

Packages Rgraphviz and rhdf5 require special libraries to be installed.
Please see the URL http://www.bioconductor.org/faq/#Other Notes for
more details on installing these packages if they fail
to install properly

Warning message:
Installation of package rhdf5 had non-zero exit status in:
installPkg(fileName, pkg, pkgVer, type, l
ib, repEntry, versForce)


Thanks for your help,

Ying Chen

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