[BioC] Loading problem with Rlibstree and microRNA packages on MacOS X 10.4
Luo Weijun
luo_weijun at yahoo.com
Sun Nov 30 03:11:32 CET 2008
Thanks, Duncan, for your timely response,
I modified the source codes for both libstree-0.4.2/src/lst_string.h and libstree-0.4.3/src/lst_string.h following your suggestion, and reinstall Rlibstree from source. This really made difference. The chunk of warning message on R_newStringSet and R_stringSetAdd functions (in stree.c file) has gone. However, the following error message still showed (below). Any ideas/suggestions? Thanks a lot!
Weijun
Building Rlibstree
** libs
** arch - ppc
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'
Warning message:
In install.packages("~/download/R/packages/Rlibstree", repos = NULL, :
installation of package '/Users/luow/download/R/packages/Rlibstree' had non-zero exit status
--- On Sat, 11/29/08, Duncan Temple Lang <duncan at wald.ucdavis.edu> wrote:
> From: Duncan Temple Lang <duncan at wald.ucdavis.edu>
> Subject: Re: [BioC] Loading problem with Rlibstree and microRNA packages on MacOS X 10.4
> To: luo_weijun at yahoo.com
> Cc: bioconductor at stat.math.ethz.ch, "Steven McKinney" <smckinney at bccrc.ca>
> Date: Saturday, November 29, 2008, 3:44 PM
> Hi Weijun
>
> Thanks for informing me about the problem.
>
> I haven't looked at the problem you got when loading
> the package, but
> rather the problem with compiling.
>
> Firstly, I would let Rlibstree build its own version of
> libstree-0.4.2 (or 0.4-3) rather than building it yourself.
> But either will work
> after the libstree source is corrected.
>
> The error when building libstree from either source is the
> lack of
> a definition for u_char or u_int. This is typically
> defined by
> the system, but not anymore on OS X. So we just need to
> define it.
>
> If you add
>
> typedef unsigned char u_char;
> typedef unsigned int u_int;
>
> to the file libstree-0.4.2/src/lst_string.h
> just before the definition
>
> struct lst_string
>
> Then things should work. They do on my systems.
>
> I'll add something to the source to check for this
> and define the types if they are not already defined.
> It won't happen in the next 2 weeks however.
>
>
> As for Rlibstree not being maintained.....
> Not certain why Steven came to that conclusion, but
> just because things aren't updated doesn't mean
> they aren't
> maintained - just that they don't need to be changed!
>
> D.
>
>
>
> Luo Weijun wrote:
> > Thanks Steven, for all the information,
> > Based on the README of Rlibstree in your message, I
> tried installed libstree-0.4.2 first, then reinstalled
> Rlibstree using: R CMD INSTALL
> --configure-args=--with-libstree=$HOME/local Rlibstree
> either from binaries or source. I still got the same loading
> error messages (and the same errors when installing
> Rlibstree from source). Different from what you have seen,
> configure and make install steps for libstree on my machine
> seemed to be okay. To me, the problem is more likely
> occurring at Rlibstree configuration and installation level.
> However, the authors of the rtracklayer package and microRNA
> package seemed to have no problem in loading Rlibstree
> package because both packages have gone through the checking
> process. Not sure what platform(s) have been checked when
> these packages were built.
> > Weijun
> >
> >
> >
> > --- On Fri, 11/28/08, Steven McKinney
> <smckinney at bccrc.ca> wrote:
> >
> >> From: Steven McKinney <smckinney at bccrc.ca>
> >> Subject: RE: [BioC] Loading problem with Rlibstree
> and microRNA packages on MacOS X 10.4
> >> To: luo_weijun at yahoo.com,
> bioconductor at stat.math.ethz.ch
> >> Date: Friday, November 28, 2008, 3:14 PM
> >> Dear Luo,
> >>
> >> The README file in the Rlibstree source directory
> >> discusses installing the software
> 'libstree'.
> >>
> >> I downloaded libstree from
> http://www.icir.org/christian/libstree/
> >> and attempted to configure and make, but libstree
> >> would not make.
> >>
> >> bash-3.2$ 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'
> >>
> >>
> >>
> >>
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> Bioconductor at stat.math.ethz.ch
> >> https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> Search the archives:
> >>
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
> > _______________________________________________
> > Bioconductor mailing list
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> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
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