[BioC] Unable to Install on SUSE Linux 8.1

[michael watson (IAH-C)]

Hi

Thanks for the attempt.... ;-)  I tried:

IAHC-LINUX03:~ # R INSTALL --configure-args=--with-hdf5=/usr/lib/ Bioconductor_1.2.tar.gz

and it got to here:

checking for H5Fopen in -lhdf5... yes
checking for hdf5.h... yes
checking hdf5 in /usr/lib/... ok

which suggests it found hdf5 of.... but then:

checking hdf5 in /usr/lib/... ok
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/lib/R/include -L/usr/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -c hdf5.c -o hdf5.o
gcc -I/usr/lib/R/include -L/usr/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -c hdf_attribs.c -o hdf_attribs.o
gcc -I/usr/lib/R/include -L/usr/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -c hdf_convert.c -o hdf_convert.o
hdf_convert.c: In function `double2int':
hdf_convert.c:23: warning: comparison between signed and unsigned
gcc -I/usr/lib/R/include -L/usr/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -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
gcc -I/usr/lib/R/include -L/usr/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -c hdf_dataspace.c -o hdf_dataspace.o
hdf_dataspace.c: In function `HDF_space_store':
hdf_dataspace.c:41: warning: comparison between signed and unsigned
hdf_dataspace.c:43: warning: comparison between signed and unsigned
gcc -I/usr/lib/R/include -L/usr/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -c hdf_datatype.c -o hdf_datatype.o
gcc -I/usr/lib/R/include -L/usr/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -c hdf_files.c -o hdf_files.o
gcc -I/usr/lib/R/include -L/usr/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -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/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -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/lib//include  -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC   -c hdf_initializer.c -o hdf_initializer.o
hdf_initializer.c: In function `H5finalize':
hdf_initializer.c:66: error: `H5I_TEMPLATE_0' undeclared (first use in this function)
hdf_initializer.c:66: error: (Each undeclared identifier is reported only once
hdf_initializer.c:66: error: for each function it appears in.)
hdf_initializer.c:67: error: `H5I_TEMPLATE_1' undeclared (first use in this function)
hdf_initializer.c:68: error: `H5I_TEMPLATE_2' undeclared (first use in this function)
hdf_initializer.c:69: error: `H5I_TEMPLATE_3' undeclared (first use in this function)
hdf_initializer.c:70: error: `H5I_TEMPLATE_4' undeclared (first use in this function)
hdf_initializer.c:71: error: `H5I_TEMPLATE_5' undeclared (first use in this function)
hdf_initializer.c:72: error: `H5I_TEMPLATE_6' undeclared (first use in this function)
hdf_initializer.c:73: error: `H5I_TEMPLATE_7' undeclared (first use in this function)
hdf_initializer.c:80: error: `H5I_TEMPLATE_MAX' undeclared (first use in this function)
make: *** [hdf_initializer.o] Error 1
ERROR: compilation failed for package 'rhdf5'


To be honest, all I want to do is install Bioconductor so I can analyse some data.  I really don't want to be bogged down in a really nasty Linux install problem that takes me days to fix, I don't have the time!  
  
Is there a release of Bioconductor that simply doesn't have rdhf5 in it, because quite frankly, it just doesn't work :-(

Thanks
Mick


-----Original Message-----
From: Jeff Gentry
To: bioconductor
Sent: 7/24/03 3:58 PM
Subject: RE: [BioC] Unable to Install on SUSE Linux 8.1



On Thu, 24 Jul 2003, michael watson (IAH-C) wrote:
> and it still fails with the same error
> Any more suggestions? :-)

Try 'R INSTALL --configure-args=--with-hdf5=<PATHTOHDF5LIBS> <Package>'

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