Hi, I am having some problems on installing bioconductor packages. I am running R 1.7.1 on RH linux 7.2. I installed Graphviz by using RPM, but not sure about HDF(I downloaded it and did what doc says I should do but rhdf5 still could not find it). Could anybody give me some idea? Thank you very much. wz > getBioC() Running getBioC version 1.2.42.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Loading required package: reposTools Creating a new generic function for "summary" in package reposTools Synching your local package management information ... Packages which have been removed: Rgraphviz RBGL Ruuid affy genefilter multtest rhdf5 Synching your local package management information ... Note: No specified download type, defaulting to Source [1] "Attempting to download Rgraphviz from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing Rgraphviz" * Installing *source* package 'Rgraphviz' ... ** libs gcc -I/opt/math/R/lib/R/include `dotneato-config --cflags` -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o In file included from /usr/include/errno.h:36, from /opt/math/R/lib/R/include/Rinternals.h:32, from common.h:10, from Rgraphviz.c:1: /usr/include/bits/errno.h:25:26: linux/errno.h: No such file or directory In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /opt/math/R/lib/R/include/Rinternals.h:38, from common.h:10, from Rgraphviz.c:1: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory In file included from Rgraphviz.c:1: common.h:19:20: render.h: No such file or directory common.h:20:19: graph.h: No such file or directory common.h:21:22: dotprocs.h: No such file or directory common.h:22:24: neatoprocs.h: No such file or directory common.h:23:20: adjust.h: No such file or directory Rgraphviz.c:2:20: circle.h: No such file or directory make: *** [Rgraphviz.o] Error 1 ERROR: compilation failed for package 'Rgraphviz' [1] "Attempting to download RBGL from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing RBGL" * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/opt/math/R/lib/R/include -I/usr/local/include -mieee-fp -IboostIncl -ftemplate-depth-30 -fPIC -g -O2 -c bfsBGL.cpp -o bfsBGL.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from boostIncl/boost/config/suffix.hpp:26, from boostIncl/boost/config.hpp:57, from RBGL.h:4, from bfsBGL.cpp:5: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory In file included from /usr/include/errno.h:36, from /opt/math/R/lib/R/include/Rmath.h:43, from bfsBGL.cpp:26: /usr/include/bits/errno.h:25:26: linux/errno.h: No such file or directory make: *** [bfsBGL.o] Error 1 ERROR: compilation failed for package 'RBGL' [1] "Attempting to download Ruuid from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing Ruuid" * Installing *source* package 'Ruuid' ... creating cache ./config.cache checking for glib-config... /usr/bin/glib-config checking how to run the C preprocessor... cc -E checking for /usr/include/unistd.h... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I/opt/math/R/lib/R/include -I/usr/include/glib-1.2 -I/usr/lib/glib/include -DHAVE_UNISTD_H=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c clear.c -o clear.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /usr/lib/glib/include/glibconfig.h:9, from /usr/include/glib-1.2/glib.h:66, from uuidP.h:24, from clear.c:14: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory make: *** [clear.o] Error 1 ERROR: compilation failed for package 'Ruuid' [1] "Attempting to download affy from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing affy" * Installing *source* package 'affy' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I/opt/math/R/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c chipbackground.c -o chipbackground.o gcc -I/opt/math/R/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c getall_locations.c -o getall_locations.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /opt/math/R/lib/R/include/R.h:34, from getall_locations.c:8: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory In file included from /usr/include/errno.h:36, from /opt/math/R/lib/R/include/Rinternals.h:32, from /opt/math/R/lib/R/include/Rdefines.h:42, from getall_locations.c:9: /usr/include/bits/errno.h:25:26: linux/errno.h: No such file or directory make: *** [getall_locations.o] Error 1 ERROR: compilation failed for package 'affy' [1] "Attempting to download genefilter from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing genefilter" * Installing *source* package 'genefilter' ... ** libs gcc -I/opt/math/R/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c genedist.c -o genedist.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /opt/math/R/lib/R/include/R.h:34, from genedist.c:27: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory In file included from /usr/include/errno.h:36, from /opt/math/R/lib/R/include/Rinternals.h:32, from genedist.c:28: /usr/include/bits/errno.h:25:26: linux/errno.h: No such file or directory make: *** [genedist.o] Error 1 ERROR: compilation failed for package 'genefilter' [1] "Attempting to download multtest from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing multtest" * Installing *source* package 'multtest' ... ** libs gcc -I/opt/math/R/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -O -Wall -DUSEDOUBLE -fPIC -g -O2 -c block_sampling_fixed.c -o block_sampling_fixed.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /opt/math/R/lib/R/include/R.h:34, from mt.h:8, from block_sampling_fixed.c:7: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory make: *** [block_sampling_fixed.o] Error 1 ERROR: compilation failed for package 'multtest' [1] "Attempting to download rhdf5 from http://www.bioconductor.org/repository/release1.2/package/Source" [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... 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' >From URL: http://www.bioconductor.org/repository/release1.2/package/Source Rgraphviz version 1.0 RBGL version 1.0-0 Ruuid version 1.0 affy version 1.2.30 genefilter version 1.0.5 multtest version 1.0.2 rhdf5 version 1.0.1 Packages that were not updated: AnnBuilder Biobase DynDoc ROC SAGElyzer affycomp affydata annotate edd geneplotter graph hexbin limma makecdfenv marrayClasses marrayInput marrayNorm marrayPlots marrayTools reposTools tkWidgets vsn widgetTools Packages Rgraphviz and rhdf5 require special libraries to be installed. Please see the URL http://www.bioconductor.org/faq.html#Other Notes for more details on installing these packages if they fail to install properly Warning messages: 1: Installation of package Rgraphviz had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 2: Installation of package RBGL had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 3: Installation of package Ruuid had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 4: Installation of package affy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 5: Installation of package genefilter had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 6: Installation of package multtest had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 7: Installation of package rhdf5 had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) > getBioC() Running getBioC version 1.2.42.... If you encounter problems, first make sure that you are running the latest version of getBioC() which can be found at: www.bioconductor.org/getBioC.R Please direct any concerns or questions to bioconductor@stat.math.ethz.ch. Synching your local package management information ... Packages which have been removed: Rgraphviz RBGL Ruuid affy genefilter multtest rhdf5 Note: No specified download type, defaulting to Source [1] "Attempting to download Rgraphviz from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing Rgraphviz" * Installing *source* package 'Rgraphviz' ... ** libs gcc -I/opt/math/R/lib/R/include `dotneato-config --cflags` -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -Wall -fPIC -g -O2 -c Rgraphviz.c -o Rgraphviz.o In file included from /usr/include/errno.h:36, from /opt/math/R/lib/R/include/Rinternals.h:32, from common.h:10, from Rgraphviz.c:1: /usr/include/bits/errno.h:25:26: linux/errno.h: No such file or directory In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /opt/math/R/lib/R/include/Rinternals.h:38, from common.h:10, from Rgraphviz.c:1: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory In file included from Rgraphviz.c:1: common.h:19:20: render.h: No such file or directory common.h:20:19: graph.h: No such file or directory common.h:21:22: dotprocs.h: No such file or directory common.h:22:24: neatoprocs.h: No such file or directory common.h:23:20: adjust.h: No such file or directory Rgraphviz.c:2:20: circle.h: No such file or directory make: *** [Rgraphviz.o] Error 1 ERROR: compilation failed for package 'Rgraphviz' [1] "Attempting to download RBGL from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing RBGL" * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/opt/math/R/lib/R/include -I/usr/local/include -mieee-fp -IboostIncl -ftemplate-depth-30 -fPIC -g -O2 -c bfsBGL.cpp -o bfsBGL.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from boostIncl/boost/config/suffix.hpp:26, from boostIncl/boost/config.hpp:57, from RBGL.h:4, from bfsBGL.cpp:5: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory In file included from /usr/include/errno.h:36, from /opt/math/R/lib/R/include/Rmath.h:43, from bfsBGL.cpp:26: /usr/include/bits/errno.h:25:26: linux/errno.h: No such file or directory make: *** [bfsBGL.o] Error 1 ERROR: compilation failed for package 'RBGL' [1] "Attempting to download Ruuid from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing Ruuid" * Installing *source* package 'Ruuid' ... creating cache ./config.cache checking for glib-config... /usr/bin/glib-config checking how to run the C preprocessor... cc -E checking for /usr/include/unistd.h... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I/opt/math/R/lib/R/include -I/usr/include/glib-1.2 -I/usr/lib/glib/include -DHAVE_UNISTD_H=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c clear.c -o clear.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /usr/lib/glib/include/glibconfig.h:9, from /usr/include/glib-1.2/glib.h:66, from uuidP.h:24, from clear.c:14: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory make: *** [clear.o] Error 1 ERROR: compilation failed for package 'Ruuid' [1] "Attempting to download affy from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing affy" * Installing *source* package 'affy' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... yes checking for zlib.h... yes checking if zlib version >= 1.1.3... yes updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I/opt/math/R/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c chipbackground.c -o chipbackground.o gcc -I/opt/math/R/lib/R/include -DHAVE_ZLIB=1 -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c getall_locations.c -o getall_locations.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /opt/math/R/lib/R/include/R.h:34, from getall_locations.c:8: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory In file included from /usr/include/errno.h:36, from /opt/math/R/lib/R/include/Rinternals.h:32, from /opt/math/R/lib/R/include/Rdefines.h:42, from getall_locations.c:9: /usr/include/bits/errno.h:25:26: linux/errno.h: No such file or directory make: *** [getall_locations.o] Error 1 ERROR: compilation failed for package 'affy' [1] "Attempting to download genefilter from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing genefilter" * Installing *source* package 'genefilter' ... ** libs gcc -I/opt/math/R/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -fPIC -g -O2 -c genedist.c -o genedist.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /opt/math/R/lib/R/include/R.h:34, from genedist.c:27: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory In file included from /usr/include/errno.h:36, from /opt/math/R/lib/R/include/Rinternals.h:32, from genedist.c:28: /usr/include/bits/errno.h:25:26: linux/errno.h: No such file or directory make: *** [genedist.o] Error 1 ERROR: compilation failed for package 'genefilter' [1] "Attempting to download multtest from http://www.bioconductor.org/repository/release1.2/package/Source" [1] "Download complete." [1] "Installing multtest" * Installing *source* package 'multtest' ... ** libs gcc -I/opt/math/R/lib/R/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp -O -Wall -DUSEDOUBLE -fPIC -g -O2 -c block_sampling_fixed.c -o block_sampling_fixed.o In file included from /usr/include/bits/posix1_lim.h:126, from /usr/include/limits.h:144, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, from /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, from /opt/math/R/lib/R/include/R.h:34, from mt.h:8, from block_sampling_fixed.c:7: /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or directory make: *** [block_sampling_fixed.o] Error 1 ERROR: compilation failed for package 'multtest' [1] "Attempting to download rhdf5 from http://www.bioconductor.org/repository/release1.2/package/Source" [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... 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' >From URL: http://www.bioconductor.org/repository/release1.2/package/Source Rgraphviz version 1.0 RBGL version 1.0-0 Ruuid version 1.0 affy version 1.2.30 genefilter version 1.0.5 multtest version 1.0.2 rhdf5 version 1.0.1 Packages that were not updated: AnnBuilder Biobase DynDoc ROC SAGElyzer affycomp affydata annotate edd geneplotter graph hexbin limma makecdfenv marrayClasses marrayInput marrayNorm marrayPlots marrayTools reposTools tkWidgets vsn widgetTools Packages Rgraphviz and rhdf5 require special libraries to be installed. Please see the URL http://www.bioconductor.org/faq.html#Other Notes for more details on installing these packages if they fail to install properly Warning messages: 1: Installation of package Rgraphviz had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 2: Installation of package RBGL had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 3: Installation of package Ruuid had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 4: Installation of package affy had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 5: Installation of package genefilter had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 6: Installation of package multtest had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) 7: Installation of package rhdf5 had non-zero exit status in: installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce) >

> from common.h:10, > from Rgraphviz.c:1: > /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or > directory > In file included from Rgraphviz.c:1: > common.h:19:20: render.h: No such file or directory > common.h:20:19: graph.h: No such file or directory > common.h:21:22: dotprocs.h: No such file or directory > common.h:22:24: neatoprocs.h: No such file or directory > common.h:23:20: adjust.h: No such file or directory > Rgraphviz.c:2:20: circle.h: No such file or directory these errors suggest that the graphviz installation from RPM is not supporting development level resources. > -IboostIncl -ftemplate-depth-30 -fPIC -g -O2 -c bfsBGL.cpp -o bfsBGL.o > In file included from /usr/include/bits/posix1_lim.h:126, > from /usr/include/limits.h:144, > from > /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:130, > from > /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/syslimits.h:7, > from > /usr/lib/gcc-lib/i386-redhat-linux/2.96/include/limits.h:11, > from boostIncl/boost/config/suffix.hpp:26, > from boostIncl/boost/config.hpp:57, > from RBGL.h:4, > from bfsBGL.cpp:5: > /usr/include/bits/local_lim.h:36:26: linux/limits.h: No such file or these errors suggest inadequacy of your linux installation. the missing files are basic development resources. you may have chosen an "end-user-only" distribution, or the linux installation is nonstandard. are you able to build R from source? i suspect not.