[BioC] Loading problem with Rlibstree and microRNA packages on MacOS X 10.4

Fri Nov 28 21:14:33 CET 2008

Dear Luo,

The README file in the Rlibstree source directory
discusses installing the software 'libstree'.

I downloaded libstree from 
http://www.icir.org/christian/libstree/
and attempted to configure and make, but libstree
would not make.

bash-3.2$ make
make  all-recursive
Making all in src
if /bin/sh ../libtool --mode=compile --tag=CC gcc-4.2 -DHAVE_CONFIG_H -I. -I. -I.. -I.. -W -Wall    -g -O2 -MT lst_stree.lo -MD -MP -MF ".deps/lst_stree.Tpo" -c -o lst_stree.lo lst_stree.c; \
	then mv -f ".deps/lst_stree.Tpo" ".deps/lst_stree.Plo"; else rm -f ".deps/lst_stree.Tpo"; exit 1; fi
 gcc-4.2 -DHAVE_CONFIG_H -I. -I. -I.. -I.. -W -Wall -g -O2 -MT lst_stree.lo -MD -MP -MF .deps/lst_stree.Tpo -c lst_stree.c  -fno-common -DPIC -o .libs/lst_stree.o
In file included from lst_structs.h:29,
                 from lst_stree.h:34,
                 from lst_stree.c:34:
lst_string.h:101: error: expected specifier-qualifier-list before 'u_char'
lst_string.h:130: error: expected specifier-qualifier-list before 'u_int'
lst_string.h:165: error: expected declaration specifiers or '...' before 'u_int'
lst_string.h:165: error: expected declaration specifiers or '...' before 'u_int'
lst_string.h:180: error: expected declaration specifiers or '...' before 'u_int'
.
.
.

Doesn't look promising.
The DESCRIPTION of Rlibstree lists Duncan Temple Lang
as the maintainer (though the date is Oct 2007)
Maintainer: Duncan Temple Lang <duncan at wald.ucdavis.edu>
so you could contact Duncan and see if he is still maintaining
this package.

The README from libstree states:
 Given that LibSTree is a self-contained library, it should build on
 any major OS out there or at least be easy to port. Reported to work:

 - Linux
 - OpenBSD

 Requirements:
 =============

 	* none, other than gcc or some other compiler.

The last date on the libstree website is Sept 2007 and
Christian Kreibich states 
"it is increasingly hard for me to find time to work on libstree"

README from Rlibstree:
-----------------------
 This is a quickly written interface to a suffix tree library to
 explore different aspects of external data and the use of suffix trees
 in R for text manipulation.  Currently, we use the libstree
 (http://www.cl.cam.ac.uk/~cpk25/libstree/, Download from
 http://www.cl.cam.ac.uk/~cpk25/downloads/libstree-0.4.0.tar.gz
 or more recently from http://www.icir.org/christian/libstree/) source
 code by Christian Kreibich. Installation of that library is relatively
 straighforward as it is stand-alone, not depending on other libraries.
 Unfortunately, to use it easily with another program, the libstree
 code should be installed.  To put it someplace for which you do not
 need special permissions, use

   cd libstree-0.4-0      # or whatever the relevant directory is.
   ./configure --prefix=$HOME/local
   make install 

 Then use

    R CMD INSTALL --configure-args=--with-libstree=$HOME/local Rlibstree 

 and that should find the relevant header and libaries files.  
 Specifically, the argument for --prefix when building and installing libstree
 should be the same as the value for --with-libstree in the R CMD INSTALL.

I think Rlibstree has not been maintained for a while
and its various parts are no longer working.

You might also need to contact the maintainer of 
the package that requires Rlibstree and let them
know of this problem.

Best

Steven McKinney

Statistician
Molecular Oncology and Breast Cancer Program
British Columbia Cancer Research Centre

email: smckinney +at+ bccrc +dot+ ca

tel: 604-675-8000 x7561

BCCRC
Molecular Oncology
675 West 10th Ave, Floor 4
Vancouver B.C. 
V5Z 1L3
Canada

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch on behalf of Luo Weijun
Sent: Fri 11/28/2008 9:44 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Loading problem with Rlibstree and microRNA packages on MacOS X 10.4

Dear all,
I called microRNA package when I tried rtracklayer package on a Mac OS X 10.4 machine. Errors produced when loading the depended package Rlibstree (see below).
I tried installed Rlibstree alone from binaries or source, both failed. Error messages (see below). suggested that R_newStringSet and R_stringSetAdd functions (in stree.c file) had problem when passing argument 1 of 'lst_string_new'. This seems to be consistent with the loading error message, but I am not sure what does it mean. Could anybody help or give any hints. Thanks a lot!
Weijun

#Loading error
Loading required package: Rlibstree
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared library '/Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/ppc/Rlibstree.so':
  dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/ppc/Rlibstree.so, 6): Symbol not found: _lst_alg_longest_common_substring
  Referenced from: /Library/Frameworks/R.framework/Resources/library/Rlibstree/libs/ppc/Rlibstree.so
  Expected in: dynamic lookup

Error: package 'Rlibstree' could not be loaded
> sessionInfo()
R version 2.8.0 (2008-10-20) 
powerpc-apple-darwin8.11.1 

locale:
C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] matchprobes_1.14.0 affy_1.20.0        Biobase_2.2.1     

loaded via a namespace (and not attached):
[1] affyio_1.10.1        preprocessCore_1.4.0

Installing error (from source)
.
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I../local/include/ -I/usr/local/include    -fPIC  -g -O2 -c prefix.c -o prefix.o
gcc -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I../local/include/ -I/usr/local/include    -fPIC  -g -O2 -c stree.c -o stree.o
stree.c: In function 'R_newStringSet':
stree.c:100: warning: passing argument 1 of 'lst_string_new' discards qualifiers from pointer target type
stree.c: In function 'R_stringSetAdd':
stree.c:316: warning: passing argument 1 of 'lst_string_new' discards qualifiers from pointer target type
gcc -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -mmacosx-version-min=10.4 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o Rlibstree.so prefix.o stree.o -L../local/lib -lstree  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
/usr/bin/libtool: for architecture cputype (16777223) cpusubtype (3) object: /usr/local/lib/libgcc_s.10.4.dylib malformed object (unknown load command 4)
make: *** [Rlibstree.so] Error 1
chmod: /Library/Frameworks/R.framework/Versions/2.8/Resources/library/Rlibstree/libs/ppc/*: No such file or directory
ERROR: compilation failed for package 'Rlibstree'
** Removing '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Rlibstree'
** Restoring previous '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Rlibstree'

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