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

[Robert Gentleman]

Hi,
  Your problems are with missing redhat libraries, and those are the 
folks who are going to have to help you. This does not really have much 
to do with Bioconductor, except in  the fact that it uses these 
libraries and you do not have them installed.



xnyang at seu.edu.cn wrote:
> 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
> 
   I don't know what packages you downloaded, for BioC, please read the 
manual page as we describe pretty clearly the recommended way to install 
Bioconductor. But many (and certainly all the ones you have had problems 
with, require other libraries to be installed).

   The errors below have to do with a package named GDD, I am not sure 
why you are attempting to install it. But it relies on the gd library, 
so that is the place to start. Google can often be of some help, as can 
the R mailing list archive.

  If you want Rgraphviz, then you will need to install graphviz from 
ATT, and make sure that you install a "developer version" as you will 
need header files (that is the case with almost all RedHat packages, you 
need to make sure the header files are installed, and in the RedHat 
world, that often means installing a developer version - but I have not 
used RedHat in years).

  best wishes
    Robert


>  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
> 
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