[BioC] Bioconductor1.6(Rgraphviz etc.) install problem with redhat 9.0

[xnyang@seu.edu.cn]

Hello all,

I want to install the R-2.1.1 and bioconductor 1.6 in Redhat 9.0,

The problems are:

1) after downloaded the R-2.1.1 packages, and % tar -xvfz, and % cd R-2.1.1
   I did % ./configure

 Source directory:          .
  Installation directory:    /usr/local
 
  C compiler:                gcc  -g -O2
  C++ compiler:              g++  -g -O2
  Fortran compiler:          g77  -g -O2
 
  Interfaces supported:      X11, tcltk
  External libraries:        readline, BLAS(generic)
  Additional capabilities:   PNG, JPEG, iconv, MBCS, NLS
  Options enabled:           R profiling
 
  Recommended packages:      yes


2) then I install R and bioconductor as 
  % make instll

  in R:
  > source("http://www.bioconductor.org/getBioC.R")
  > getBioC(groupName='all', lib=.libPaths()[1])

  8 packages were failed, which were: 
  "GDD","RCurl","rhdf5","xcms","SSOAP", "GeneTraffic", "KEGGSOAP", "Rgraphviz"


  Please help to fix them, I want to use the package "Rgraphviz" indeed.
  I think "Rgraphviz", "SSOAP", "GeneTraffic" and "KEGGSOAP" are depended on "RCurl", 
  whose error may because of the error occuring in "rhdf5".  
   
  But I'm a new hander in Linux system , please help!


  The detailed error messages were:

* Installing *source* package 'GDD' ...
checking for gcc... gcc
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for string.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking whether time.h and sys/time.h may both be included... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking return type of signal handlers... void
checking for memset... yes
checking for mkdir... yes
checking for rmdir... yes
checking for gdlib-config... /usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/bin:ext/bin:ext
./configure: line 1: /usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/bin:ext/bin:ext: No such file or directory
./configure: line 1: /usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/bin:ext/bin:ext: No such file or directory
./configure: line 1: /usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/bin:ext/bin:ext: No such file or directory
./configure: line 1: /usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/bin:ext/bin:ext: No such file or directory
./configure: line 1: /usr/kerberos/sbin:/usr/kerberos/bin:/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/X11R6/bin:/root/bin:/usr/local/bin:ext/bin:ext: No such file or directory
libgd-flags according to gdlib-config:
      
if that is not correct, fix your gd installation
checking gd.h usability... yes
checking gd.h presence... yes
checking for gd.h... yes
checking for gdImageCreateFromPng in -lgd... yes
checking usability of FreeType in GD... yes
checking whether GD programs can be compiled... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/gddconfig.h
** libs
gcc -I/usr/local/lib/R/include -DHAVE_GDDCONFIG_H -I. -Iinclude
-I/usr/local/include  -g -O2 -fPIC  -g -O2 -c GDD.c -o GDD.o
gcc -I/usr/local/lib/R/include -DHAVE_GDDCONFIG_H -I. -Iinclude
-I/usr/local/include  -g -O2 -fPIC  -g -O2 -c GDDtalk.c -o GDDtalk.o
GDDtalk.c: In function `sendGC':
GDDtalk.c:135: warning: assignment makes pointer from integer without a cast
GDDtalk.c: In function `GDD_Line':
GDDtalk.c:302: `gdAntiAliased' undeclared (first use in this function)
GDDtalk.c:302: (Each undeclared identifier is reported only onceGDDtalk.c:302: for each function it appears in.)
GDDtalk.c: In function `GDD_Open':
GDDtalk.c:384: warning: assignment makes pointer from integer without a cast
GDDtalk.c: In function `GDD_Polygon':
GDDtalk.c:418: `gdAntiAliased' undeclared (first use in this function)
GDDtalk.c: In function `GDD_Polyline':
GDDtalk.c:446: `gdAntiAliased' undeclared (first use in this function)
GDDtalk.c: In function `gddSetFTFontPath':
GDDtalk.c:573: `gdFTStringExtra' undeclared (first use in this function)
GDDtalk.c:573: parse error before "se"
GDDtalk.c:575: `se' undeclared (first use in this function)
GDDtalk.c:579: `gdFTEX_RETURNFONTPATHNAME' undeclared (first use in this function)
GDDtalk.c:579: `gdFTEX_FONTCONFIG' undeclared (first use in this function)
GDDtalk.c: In function `gdd_look_up_font':
GDDtalk.c:644: `gdFTStringExtra' undeclared (first use in this function)
GDDtalk.c:644: parse error before "se"
GDDtalk.c:645: `se' undeclared (first use in this function)
GDDtalk.c:647: `gdFTEX_RETURNFONTPATHNAME' undeclared (first use in this function)
GDDtalk.c:647: `gdFTEX_FONTCONFIG' undeclared (first use in this function)
make: *** [GDDtalk.o] Error 1
ERROR: compilation failed for package 'GDD'
** Removing '/usr/local/lib/R/library/GDD'
** Restoring previous '/usr/local/lib/R/library/GDD'



* Installing *source* package 'RCurl' ...
checking for curl-config... /usr/bin/curl-config
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 suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
No libidn field in version structure.
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/usr/local/lib/R/include -Wall   -I/usr/local/include   -fPIC  -g -O2 -c curl.c -o curl.o
curl.c:28: parse error before '*' token
curl.c: In function `R_curl_easy_init':
curl.c:43: `CURLOPT_HTTPAUTH' undeclared (first use in this function)
curl.c:43: (Each undeclared identifier is reported only once
curl.c:43: for each function it appears in.)
curl.c:43: `CURLAUTH_ANY' undeclared (first use in this function)
curl.c: In function `R_curl_easy_setopt':
curl.c:153: warning: implicit declaration of function `curl_easy_strerror'
curl.c:154: warning: format argument is not a pointer (arg 7)
curl.c: In function `R_curl_version_info':
curl.c:239: `curl_version_info_data' undeclared (first use in this function)
curl.c:239: `data' undeclared (first use in this function)
curl.c:240: warning: implicit declaration of function `curl_version_info'
curl.c: In function `R_curl_escape':
curl.c:326: warning: implicit declaration of function `curl_free'
curl.c: At top level:
curl.c:660: parse error before '*' token
curl.c: In function `RCurlVersionInfoToR':
curl.c:667: `d' undeclared (first use in this function)
make: *** [curl.o] Error 1
ERROR: compilation failed for package 'RCurl'
** Removing '/usr/local/lib/R/library/RCurl'
** Restoring previous '/usr/local/lib/R/library/RCurl'



* 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 suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for hdf5... yes
checking for H5Fopen in -lhdf5... no
checking hdf5.h usability... no
checking hdf5.h presence... 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'



* Installing *source* package 'xcms' ...
** libs
gcc -I/usr/local/lib/R/include -I/usr/local/include -I/sw/include -I/usr/local/include   -fPIC  -g -O2 -c netCDF.c -o netCDF.o
netCDF.c:2:20: netcdf.h: No such file or directory
netCDF.c: In function `NetCDFStrError':
netCDF.c:8: warning: passing arg 1 of `strlen' makes pointer from integer without a cast
netCDF.c:8: warning: passing arg 2 of `memcpy' makes pointer from integer without a cast
netCDF.c:8: warning: passing arg 2 of `strncpy' makes pointer from integer without a cast
netCDF.c:8: warning: passing arg 2 of `strncpy' makes pointer from integer without a cast
netCDF.c: In function `NetCDFOpen':
netCDF.c:13: `NC_NOWRITE' undeclared (first use in this function)
netCDF.c:13: (Each undeclared identifier is reported only once
netCDF.c:13: for each function it appears in.)
netCDF.c: In function `NetCDFVarLen':
netCDF.c:28: `NC_MAX_VAR_DIMS' undeclared (first use in this function)
make: *** [netCDF.o] Error 1
ERROR: compilation failed for package 'xcms'
** Removing '/usr/local/lib/R/library/xcms'
** Restoring previous '/usr/local/lib/R/library/xcms'



* Installing *source* package 'Rgraphviz' ...
checking for graphviz... checking for dotneato-config... not found
failed
configure: error: please specify a valid path to 'dotneato-config' version >= 1.12 using --with-graphviz=DIR
ERROR: configuration failed for package 'Rgraphviz'



xinan