[BioC] Unable to Install on SUSE Linux 8.1

[James MacDonald]

You could simply install the individual packages that you want instead
of the whole Bioconductor package. Either download separately or use
getBioC. The problem with getBioC is that I don't know if it tells you a
priori exactly what you will be getting (e.g., if you use
libName="affy", you get lots more than just the affy package).

Jim



James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "michael watson (IAH-C)" <michael.watson at bbsrc.ac.uk> 07/25/03
04:38AM >>>
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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