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 _________________________________________________________________ Use custom emotions -- try MSN Messenger 6.0! http://www.msnmessenger-download.com/tracking/reach_emoticon

I am new to R and Bioconductor, and really need your help. I downloaded 5-1.6.0-linux-gcc3.2.2.tar.gz from HDF5 site. I decompressed the files and put the folder in /usr/lib. I followed the README file and cd into /bin. Then, I typed ./h5redeploy and answered yes to the questions. It seemed go well since I got no error message. But when I use getBioC(Ą°progĄą) to install the Rhdf5 package, 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 Warning message: Installation of package rhdf5 had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, l ib, repEntry, versForce) Any suggestion is highly appreciated. Thanks, Ying _________________________________________________________________ Get a FREE computer virus scan online from McAfee.