Skip to content

[Bioc-devel] RBGL 1.12 compile/install issue

4 messages · Li.Long at isb-sib.ch, Ben Snyder, Seth Falcon

Original
Li.Long at isb-sib.ch
# 
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
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:
Li.Long at isb-sib.ch
# 
......
If this is really what's used, you SHOULD get

g++ -shared -o RBGL.so ....

You could try to modify the 1st line in .../R-2.5.0/bin/INSTALL to

#! /bin/sh -xv

to turn on the echos to see what happens when running
    .../R-2.5.0/bin/R CMD INSTALL .../RBGL

Just for your reference, here's what I see from my run:

......
++ sh /home/vital-it/lilong/R-src/R-2.5.0/bin/SHLIB -o RBGL.so bbc.cpp
cliques.cpp clusteringCoef.cpp hcs.cpp incrConnComp.cpp interfaces.cpp
layout.cpp mincut.cpp minST.cpp ordering.cpp shortestPath.cpp sna.cpp
transitive_closure.cpp wavefront.cpp
g++ -shared -L/usr/local/lib -o RBGL.so bbc.o cliques.o clusteringCoef.o
hcs.o incrConnComp.o interfaces.o layout.o mincut.o minST.o ordering.o
shortestPath.o sna.o transitive_closure.o wavefront.o
......

You can see that SHLIB is expanded to
     g++ -shared -L/usr/local/lib
correctly.

Let me know what I could help.

Li
Seth Falcon
# 
It would be very strange if the solution required editing one of the
scripts in RHOME/bin such as SHLIB.  One other place to look is in
RHOME/etc/Makeconf which controls various compilation options for
installing packages.

+ seth