[BioC] Problems building Bioconductor 1.5 on RHAW 3

[Steve Simmons]

I'm having problems building the bioconductor 1.5 release on
RedHat Advanced Workstation 1.5.  There are four failures which
I've not been able to remedy and either have questions on or
just want to report a bug.  All the rest I've been able to
work around or fix in fairly short order.


Graphviz builds fail:

I've tried three different versions of graphviz for Rgraphviz
to build against -- 1.4.1, 1.8.1, and 2.0.1.  In all three cases
I used the Fedora core 1 rpms from the graphviz site.

Rgraphviz fails to build against 2.0.1 with a probably bogus complaint
that it requires 'dotneato-config' version 1.0 or later.  If you do
'dotneato-config --version' it reports version 2.0.

Backreving to 1.18.1 gets an acceptable dotneato-config version,
but generates warnings and errors:

    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    gcc -I/usr/lib/R/include -I/usr/include/graphviz  -I/usr/local/include  -Wall -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c Rgraphviz.c -o Rgraphviz.o
    In file included from /usr/include/graphviz/render.h:46,
		     from common.h:22,
		     from Rgraphviz.c:1:
    /usr/include/graphviz/macros.h:34:1: warning: "NEW" redefined
    In file included from common.h:13,
		     from Rgraphviz.c:1:
    /usr/lib/R/include/Rdefines.h:129:1: warning: this is the location of the previous definition
    In file included from Rgraphviz.c:1:
    common.h:63: conflicting types for `neatoLayout'
    /usr/include/graphviz/neatoprocs.h:53: previous declaration of `neatoLayout'
    make: *** [Rgraphviz.o] Error 1
    ERROR: compilation failed for package 'Rgraphviz'
    From URL:  http://www.bioconductor.org/repository/release1.5/package/Source
	    Rgraphviz version 1.5.0

Backreving to 1.14.1 gets an acceptable NEW, but fails to find the
libraries:

    configure: creating ./config.status
    config.status: creating src/Makevars
    ** libs
    gcc -I/usr/lib/R/include -I/usr/include/graphviz  -I/usr/local/include  -Wall -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c Rgraphviz.c -o Rgraphviz.o
    In file included from /usr/include/graphviz/render.h:45,
		     from common.h:22,
		     from Rgraphviz.c:1:
    /usr/include/graphviz/macros.h:34:1: warning: "NEW" redefined
    In file included from common.h:13,
		     from Rgraphviz.c:1:
    /usr/lib/R/include/Rdefines.h:129:1: warning: this is the location of the previous definition
    gcc -I/usr/lib/R/include -I/usr/include/graphviz  -I/usr/local/include  -Wall -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c RgraphvizInit.c -o RgraphvizInit.o
    In file included from /usr/include/graphviz/render.h:45,
		     from common.h:22,
		     from RgraphvizInit.c:1:
    /usr/include/graphviz/macros.h:34:1: warning: "NEW" redefined
    In file included from common.h:13,
		     from RgraphvizInit.c:1:
    /usr/lib/R/include/Rdefines.h:129:1: warning: this is the location of the previous definition
    gcc -shared -L/usr/local/lib -o Rgraphviz.so Rgraphviz.o RgraphvizInit.o -Wl -ldotneato -lm
    /usr/bin/ld: cannot find -ldotneato
    collect2: ld returned 1 exit status
    make: *** [Rgraphviz.so] Error 1
    ERROR: compilation failed for package 'Rgraphviz'

I didn't bother trying 1.16-1, and 1.12 was not available in an RPM
package that I'd trust.  So before trying to build it from scratch,
I'd like to know if there is a particular version of graphviz that
people are using and (especially on Linux) if they built it themselves.


RCurl builds fail:

RCurl fails to build with compilation errors:

    [1] "Attempting to download RCurl from http://www.bioconductor.org/repository/Omegahat/"
    [1] "Download complete."
    [1] "Installing RCurl"
    * 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/lib/R/include -Wall   -I/usr/local/include   -fPIC  -O2 -g -pipe -march=i386 -mcpu=i686 -c curl.c -o curl.o
    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 `RCurlVersionInfoToR':
    curl.c:679: structure has no member named `ares'
    curl.c:679: structure has no member named `ares'
    curl.c:680: structure has no member named `ares_num'
    make: *** :s:^.*$:/*&*/:
    aurl.o] Error 1
    ERROR: compilation failed for package 'RCurl'

At first examination I'd guess that there's some sort of version conflict
with a libidn or that I don't have it installed, but the only libidn I
found via google is alpha-quality software on the GNU ftp servers.  Is
that the library needed, and if so (since there are a zillion alpha
versions), which versions are people having luck with>


SSOAP not found to install:

SSOAP isn't found by the install process:

    Note: Package SSOAP not found in any known repository.

Later it notes:

    Package SSOAP version 0.2-1 depends on RCurl

Anybody know where/what it is?


KEGGSOAP fails to install without SSOAP:

KEGGSOAP is downloaded successfully, but cannot be installed because
it requires SSOAP.


I have all of this in excruciatingly detailed installation logs if
anybody wants more data.


Advance thanks,

Steve