Hi I am running R version 1.7.1 on SUSE Linux 8.1 I downloaded the tarball and typed: R CMD INSTALL Bioconductor_1.2.tar.gz It got so far and then: * 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... no checking for hdf5.h... no checking hdf5 in /sw... failed configure: error: please specify a valid hdf5 installation with --with-hdf5=DIR ERROR: configuration failed for package 'rhdf5' Any help? Thanks in advance :-D Mick

You need hdf5 http://hdf.ncsa.uiuc.edu/HDF5/release/obtain5.html 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@bbsrc.ac.uk> 07/24/03 07:44AM >>> Hi I am running R version 1.7.1 on SUSE Linux 8.1 I downloaded the tarball and typed: R CMD INSTALL Bioconductor_1.2.tar.gz It got so far and then: * 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... no checking for hdf5.h... no checking hdf5 in /sw... failed configure: error: please specify a valid hdf5 installation with --with-hdf5=DIR ERROR: configuration failed for package 'rhdf5' Any help? Thanks in advance :-D Mick _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

I HAVE hdf5: IAHC-LINUX03:~ # rpm -q -a | grep hdf hdf5-1.4.0-99 and it still fails with the same error Any more suggestions? :-) -----Original Message----- From: James MacDonald To: michael.watson@bbsrc.ac.uk; bioconductor@stat.math.ethz.ch Sent: 7/24/03 3:01 PM Subject: Re: [BioC] Unable to Install on SUSE Linux 8.1 You need hdf5 http://hdf.ncsa.uiuc.edu/HDF5/release/obtain5.html 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@bbsrc.ac.uk> 07/24/03 07:44AM >>> Hi I am running R version 1.7.1 on SUSE Linux 8.1 I downloaded the tarball and typed: R CMD INSTALL Bioconductor_1.2.tar.gz It got so far and then: * 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... no checking for hdf5.h... no checking hdf5 in /sw... failed configure: error: please specify a valid hdf5 installation with --with-hdf5=DIR ERROR: configuration failed for package 'rhdf5' Any help? Thanks in advance :-D Mick _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

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>' _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

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@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>' _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor