[Bioc-devel] RBGL 1.12 compile/install issue

[Ben Snyder]

Hello Li, hello list

I don't know what to copy from SHLIB, though here's my guess.

Variables:
objs=
shlib=
makefiles="-f ${R_SHARE_DIR}/make/shlib.mk"
shlib_libadd=''
with_cxx=false
with_f77=false
with_f9x=false
with_objc=false
with_objcxx=false
pkg_libs=

This looks important:
makeargs="SHLIB=\"${shlib}\""
if ${with_f9x}; then
    makeargs="SHLIB_LDFLAGS='\$(SHLIB_FCLDFLAGS)' ${makeargs}"
    makeargs="SHLIB_LD='\$(SHLIB_FCLD)' ${makeargs}"
else
  if ${with_cxx}; then
    makeargs="SHLIB_LDFLAGS='\$(SHLIB_CXXLDFLAGS)' ${makeargs}"
    makeargs="SHLIB_LD='\$(SHLIB_CXXLD)' ${makeargs}"
  fi
  if ${with_f77}; then
    if ${with_objc}; then
      shlib_libadd="\$(OBJC_LIBS) ${shlib_libadd}"
    fi
    if test -z "${shlib_libadd}"; then
      makeargs="${makeargs} SHLIB_LIBADD='\$(FLIBS)'"
    else
      makeargs="${makeargs} SHLIB_LIBADD='\$(FLIBS) ${shlib_libadd}'"
    fi
  else
    if ${with_objc}; then
      makeargs="${makeargs} SHLIB_LIBADD='\$(OBJC_LIBS)'"
    fi
  fi
fi
if test -n "${pkg_libs}"; then
  makeargs="${makeargs} PKG_LIBS='${pkg_libs}'"
fi

And the final line:
eval ${MAKE} ${makefiles} ${makeargs} ${makeobjs}

Let me know if I'm missing something here.

What also looks pertinent is my shlib.mk:
## ${R_HOME}/share/make/shlib.mk

include $(R_HOME)/etc${R_ARCH}/Makeconf

$(SHLIB): $(OBJECTS)
        $(SHLIB_LINK) -o $@ $(OBJECTS) $(ALL_LIBS)

and my etc/Makeconf:
SHLIB_CFLAGS =
SHLIB_CXXFLAGS =
SHLIB_CXXLD = g++
SHLIB_CXXLDFLAGS =
SHLIB_EXT = .so
SHLIB_FCLD = g77
SHLIB_FCLDFLAGS = -shared
SHLIB_FFLAGS =
SHLIB_LD = gcc -std=gnu99
SHLIB_LDFLAGS = -shared
SHLIB_LIBADD =
SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS)

Right off the top, it looks to me that my with_cxx, with_f77 and 
with_f9x variables are set incorrectly.  Does anything else seem amiss?

Thanks,
Ben

Li.Long at isb-sib.ch wrote:
> Hi, Ben,
>
> Could you take a look at your .../R-2.5.0/bin/SHLIB?  This is what
> packages use to build their shared libs.  This script is auto-generated
> based on
>    R-2.5.0/src/scripts/SHLIB.in
> when you install R.  There's nothing special in generating .so in RBGL
> compared with generating .so in other packages.
>
> I don't have access to CentOS, but I suspect that during your R
> installation, the "configure"-step didn't set the "-shared" flag properly.
>  In that case, the fix will have to go to R installation to handle CentOS
> correctly.
>
> Let me know.  Thanks.
>
> Li
>
>   
>> Hello folks
>>
>> No question here, just information.  I've noticed a small problem when
>> trying to install RBGL 1.12 on a Linux platform.  The compilation steps
>> work fine, until the .so object is to be built.  There is no -shared
>> flag, so it tries to build a standalone executable instead of a shared
>> object.
>>
>> My system details are:
>> CentOS 4.5
>> gcc/g++ version 3.4.6 (Also tried with 4.1)
>> R version 2.5.0
>>
>> This issue was fixed easily enough by adding the line 'PKG_LIBS=-shared'
>> to the src/Makevars file, then re-tarring the package
>>
>> Sincerely,
>> Ben Snyder
>>
>>
>>     
>
>
>