Hi Duncan, I thought Rlibstree might not be maintained as the README states "This is a quickly written interface... ", has no vignette or pdf, and references an older version of libstree "libstree-0.4.0.tar.gz" so it wasn't clear when this package was last touched. My apologies for that judgment. Thanks for your information on patching the libstree header file. After adding the requisite lines, I can configure and make libstree-0.4.3 I then installed Rlibstree from binaries, but when I try to load it I get this error message > require("Rlibstree") Loading required package: Rlibstree Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/Resou rces/library/Rlibstree/libs/ppc/Rlibstree.so': dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibstree/l ibs/ppc/Rlibstree.so, 6): Symbol not found: _lst_alg_longest_common_substring Referenced from: /Library/Frameworks/R.framework/Resources/library/R libstree/libs/ppc/Rlibstree.so Expected in: dynamic lookup > sessionInfo() R version 2.8.0 Patched (2008-11-06 r46845) powerpc-apple-darwin9.5.0 locale: en_CA.UTF-8/en_CA.UTF-8/C/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] fortunes_1.3-5 matchprobes_1.14.0 affy_1.20.0 org.Hs.eg.db_2.2.6 humanStemCell_0.2.0 [6] hgu133plus2.db_2.2.5 RSQLite_0.7-1 DBI_0.2-4 AnnotationDbi_1.4.1 limma_2.16.3 [11] genefilter_1.22.0 survival_2.34-1 rtracklayer_1.2.2 RCurl_0.92-0 Biobase_2.2.1 loaded via a namespace (and not attached): [1] Biostrings_2.10.8 IRanges_1.0.5 Matrix_0.999375-16 XML_1.98-1 affyio_1.10.1 [6] annotate_1.20.1 grid_2.8.0 lattice_0.17-15 preprocessCore_1.4.0 rJava_0.6-0 Does this bit of the error message suggest what the problem might be? "Symbol not found: _lst_alg_longest_common_substring" I then tried installing from source, but during the installation, libstree is recompiled from the local version included with the Rlibstree source. I had to specify a flag "CC=gcc-4.2" in my manual compilation, but haven't yet figured out how to specify this when installing Rlibstree from source. So installing from source has not yet been successful either. (Output from R.app GUI window of install is included at end of email). Any further guidance appreciated. 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: Luo Weijun [mailto:luo_weijun@yahoo.com] Sent: Sat 11/29/2008 6:11 PM To: Duncan Temple Lang Cc: bioconductor at stat.math.ethz.ch; Steven McKinney Subject: Re: [BioC] Loading problem with Rlibstree and microRNA packages on MacOS X 10.4 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/li brary/Rlibstree' ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.8/Re sources/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/pp c/Rlibstree.so': > >> > dlopen(/Library/Frameworks/R.framework/Resources/library/Rlibstree/l ibs/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/Rlibs tree/libs/ppc/*: > >> No such file or directory > >> ERROR: compilation failed for package > 'Rlibstree' > >> ** Removing > >> > '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Rlib stree' > >> ** Restoring previous > >> > '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Rlib stree' > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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 > > 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 * Installing *source* package 'Rlibstree' ... Using version 0.4.2 of libstree source included with this R package Need to compile the source. This may take a few moments. checking for a BSD-compatible install... /usr/bin/install -c checking whether build environment is sane... yes checking for gawk... awk checking whether make sets $(MAKE)... yes shtool:echo:Warning: unable to determine terminal sequence for bold mode shtool:echo:Warning: unable to determine terminal sequence for bold mode checking for gcc... gcc checking for C compiler default output file name... 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 for style of include used by make... GNU checking dependency style of gcc... gcc3 checking whether make sets $(MAKE)... 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checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes configure: creating libtool appending configuration tag "CXX" to libtool checking for ld used by g++... /usr/libexec/gcc/powerpc-apple- darwin9/4.0.1/ld checking if the linker (/usr/libexec/gcc/powerpc-apple- darwin9/4.0.1/ld) is GNU ld... no checking whether the g++ linker (/usr/libexec/gcc/powerpc-apple- darwin9/4.0.1/ld) supports shared libraries... yes checking for g++ option to produce PIC... -fno-common checking if g++ PIC flag -fno-common works... rm: conftest.dSYM: is a directory yes checking if g++ supports -c -o file.o... rm: conftest.dSYM: is a directory yes checking whether the g++ linker (/usr/libexec/gcc/powerpc-apple- darwin9/4.0.1/ld) supports shared libraries... yes checking dynamic linker characteristics... darwin9.5.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes appending configuration tag "F77" to libtool checking if libtool supports shared libraries... yes checking whether to build shared libraries... no checking whether to build static libraries... yes checking for gfortran option to produce PIC... -fno-common checking if gfortran PIC flag -fno-common works... rm: conftest.dSYM: is a directory yes checking if gfortran supports -c -o file.o... rm: yes checking whether the gfortran linker (/usr/libexec/gcc/powerpc-apple- darwin9/4.0.1/ld) supports shared libraries... conftest.dSYM: is a directory yes checking dynamic linker characteristics... darwin9.5.0 dyld checking how to hardcode library paths into programs... immediate checking whether stripping libraries is possible... yes checking for gtkdoc-mkdb... false configure: creating ./config.status config.status: creating Makefile config.status: creating src/Makefile config.status: creating test/Makefile config.status: creating docs/Makefile config.status: creating config.h config.status: executing depfiles commands libstree Configuration Summary ==================================================== Setup finished. Now run: $ make # make install (or use gmake when make on your platform isn't GNU make) make all-recursive Making all in src if /bin/sh ../libtool --mode=compile --tag=CC gcc -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 -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 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: syntax error before 'u_char' lst_string.h:101: warning: no semicolon at end of struct or union lst_string.h:103: warning: type defaults to 'int' in declaration of 'num_items' lst_string.h:103: warning: data definition has no type or storage class lst_string.h:104: error: syntax error before 'item_size' lst_string.h:104: warning: type defaults to 'int' in declaration of 'item_size' lst_string.h:104: warning: data definition has no type or storage class lst_string.h:107: error: syntax error before '}' token lst_string.h:130: error: syntax error before 'u_int' lst_string.h:130: warning: no semicolon at end of struct or union lst_string.h:136: warning: type defaults to 'int' in declaration of 'end_index' lst_string.h:136: warning: data definition has no type or storage class lst_string.h:137: error: syntax error before 'end_index_local' lst_string.h:137: warning: type defaults to 'int' in declaration of 'end_index_local' lst_string.h:137: warning: data definition has no type or storage class lst_string.h:143: error: syntax error before 'extra_index' lst_string.h:143: warning: type defaults to 'int' in declaration of 'extra_index' lst_string.h:143: warning: data definition has no type or storage class lst_string.h:165: error: syntax error before 'u_int' lst_string.h:180: error: syntax error before 'u_int' lst_string.h:217: error: syntax error before 'lst_string_get_length' lst_string.h:217: warning: type defaults to 'int' in declaration of 'lst_string_get_length' lst_string.h:217: warning: data definition has no type or storage class lst_string.h:228: error: syntax error before 'u_int' lst_string.h:254: error: syntax error before 'u_int' lst_string.h:271: error: syntax error before 'u_int' lst_string.h:289: error: syntax error before 'lst_string_items_common' lst_string.h:289: error: syntax error before 'u_int' lst_string.h:291: warning: type defaults to 'int' in declaration of 'lst_string_items_common' lst_string.h:291: warning: data definition has no type or storage class In file included from lst_stree.h:34, from lst_stree.c:34: lst_structs.h:47: error: field 'range' has incomplete type lst_structs.h:55: error: syntax error before 'u_int' lst_structs.h:55: warning: no semicolon at end of struct or union lst_structs.h:67: error: 'index' redeclared as different kind of symbol lst_structs.h:68: error: syntax error before 'id' lst_structs.h:68: warning: type defaults to 'int' in declaration of 'id' lst_structs.h:68: warning: data definition has no type or storage class lst_structs.h:71: error: syntax error before 'bus_visited' lst_structs.h:71: warning: type defaults to 'int' in declaration of 'bus_visited' lst_structs.h:71: warning: data definition has no type or storage class lst_structs.h:79: error: syntax error before 'u_int' lst_structs.h:79: warning: no semicolon at end of struct or union lst_structs.h:96: error: syntax error before 'u_int' lst_structs.h:96: warning: no semicolon at end of struct or union lst_structs.h:103: warning: type defaults to 'int' in declaration of 'phase' lst_structs.h:103: warning: data definition has no type or storage class lst_structs.h:113: error: syntax error before 'ext' lst_structs.h:113: warning: type defaults to 'int' in declaration of 'ext' lst_structs.h:113: warning: data definition has no type or storage class lst_structs.h:119: error: conflicting types for 'leafs' lst_structs.h:61: error: previous declaration of 'leafs' was here lst_structs.h:143: error: syntax error before 'visitors' lst_structs.h:143: warning: type defaults to 'int' in declaration of 'visitors' lst_structs.h:143: error: conflicting types for 'visitors' lst_structs.h:70: error: previous declaration of 'visitors' was here lst_structs.h:143: warning: data definition has no type or storage class In file included from lst_stree.c:36: lst_algorithms.h:107: error: syntax error before 'lst_alg_set_visitors' lst_algorithms.h:107: warning: type defaults to 'int' in declaration of 'lst_alg_set_visitors' lst_algorithms.h:107: warning: data definition has no type or storage class lst_algorithms.h:128: error: syntax error before 'u_int' lst_algorithms.h:149: error: syntax error before 'u_int' lst_stree.c:55: error: syntax error before 'u_int' lst_stree.c:55: warning: no semicolon at end of struct or union lst_stree.c:57: warning: type defaults to 'int' in declaration of 'LST_PathEnd' lst_stree.c:57: warning: data definition has no type or storage class lst_stree.c:64: error: syntax error before 'u_int' lst_stree.c: In function 'edge_new': lst_stree.c:76: error: 'src_node' undeclared (first use in this function) lst_stree.c:76: error: (Each undeclared identifier is reported only once lst_stree.c:76: error: for each function it appears in.) lst_stree.c:77: error: 'dst_node' undeclared (first use in this function) lst_stree.c:79: error: 'string' undeclared (first use in this function) lst_stree.c:80: error: 'start_index' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:98: error: syntax error before 'u_int' lst_stree.c: In function 'edge_leaf_new': lst_stree.c:100: error: 'src_node' undeclared (first use in this function) lst_stree.c:100: error: 'dst_node' undeclared (first use in this function) lst_stree.c:100: error: 'string' undeclared (first use in this function) lst_stree.c:100: error: 'start_index' undeclared (first use in this function) lst_stree.c:108: error: 'tree' undeclared (first use in this function) lst_stree.c: In function 'node_new': lst_stree.c:129: error: nested functions are disabled, use -fnested- functions to re-enable lst_stree.c:129: error: syntax error before 'id' lst_stree.c:132: error: invalid application of 'sizeof' to incomplete type 'LST_Node' lst_stree.c:140: error: dereferencing pointer to incomplete type lst_stree.c:141: error: dereferencing pointer to incomplete type lst_stree.c:142: error: dereferencing pointer to incomplete type lst_stree.c: In function 'node_free': lst_stree.c:156: error: dereferencing pointer to incomplete type lst_stree.c:156: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:160: error: dereferencing pointer to incomplete type lst_stree.c:162: error: dereferencing pointer to incomplete type lst_stree.c:163: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c: At top level: lst_stree.c:172: error: syntax error before 'u_int' lst_stree.c: In function 'node_find_edge_with_startitem': lst_stree.c:176: error: 'node' undeclared (first use in this function) lst_stree.c:176: error: 'string' undeclared (first use in this function) lst_stree.c: In function 'stree_remove_edge': lst_stree.c:206: error: dereferencing pointer to incomplete type lst_stree.c:209: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c: In function 'stree_extend_label_at_leaf': lst_stree.c:222: error: dereferencing pointer to incomplete type lst_stree.c:222: error: dereferencing pointer to incomplete type lst_stree.c: At top level: lst_stree.c:227: error: syntax error before '*' token lst_stree.c: In function 'stree_path_end_node': lst_stree.c:229: error: 'end' undeclared (first use in this function) lst_stree.c:230: error: 'node' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:235: error: syntax error before '*' token lst_stree.c: In function 'stree_path_end_edge': lst_stree.c:237: error: 'end' undeclared (first use in this function) lst_stree.c:238: error: 'edge' undeclared (first use in this function) lst_stree.c:239: error: 'offset' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:244: error: syntax error before '*' token lst_stree.c: In function 'stree_path_end_advance': lst_stree.c:246: error: 'end' undeclared (first use in this function) lst_stree.c:251: error: 'edge' undeclared (first use in this function) lst_stree.c:260: error: 'u_int' undeclared (first use in this function) lst_stree.c:260: error: syntax error before 'lst_edge_get_length' lst_stree.c: At top level: lst_stree.c:280: error: syntax error before 'stree_follow_string_slow' lst_stree.c:281: error: syntax error before 'LST_PathEnd' lst_stree.c:282: warning: return type defaults to 'int' lst_stree.c: In function 'stree_follow_string_slow': lst_stree.c:284: error: 'u_int' undeclared (first use in this function) lst_stree.c:284: error: syntax error before 'items_todo' lst_stree.c:286: error: 'tree' undeclared (first use in this function) lst_stree.c:286: error: 'node' undeclared (first use in this function) lst_stree.c:286: error: 'string' undeclared (first use in this function) lst_stree.c:286: error: 'end' undeclared (first use in this function) lst_stree.c:293: error: 'items_todo' undeclared (first use in this function) lst_stree.c:301: error: 'items_done' undeclared (first use in this function) lst_stree.c:311: error: 'common' undeclared (first use in this function) lst_stree.c:316: error: syntax error before 'lst_edge_get_length' lst_stree.c: At top level: lst_stree.c:329: warning: type defaults to 'int' in declaration of 'stree_path_end_node' lst_stree.c:329: warning: parameter names (without types) in function declaration lst_stree.c:329: error: conflicting types for 'stree_path_end_node' lst_stree.c:228: error: previous definition of 'stree_path_end_node' was here lst_stree.c:329: warning: data definition has no type or storage class lst_stree.c:330: error: syntax error before 'return' lst_stree.c:347: error: syntax error before 'LST_PathEnd' lst_stree.c: In function 'stree_follow_string': lst_stree.c:351: error: 'u_int' undeclared (first use in this function) lst_stree.c:351: error: syntax error before 'items_todo' lst_stree.c:353: error: 'tree' undeclared (first use in this function) lst_stree.c:353: error: 'node' undeclared (first use in this function) lst_stree.c:353: error: 'skipstring' undeclared (first use in this function) lst_stree.c:353: error: 'end' undeclared (first use in this function) lst_stree.c:376: error: 'items_todo' undeclared (first use in this function) lst_stree.c:391: error: syntax error before 'edge_len' lst_stree.c:393: error: 'items_done' undeclared (first use in this function) lst_stree.c:401: error: 'edge_len' undeclared (first use in this function) lst_stree.c:401: error: syntax error before 'lst_edge_get_length' lst_stree.c:435: error: 'common' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:464: error: syntax error before 'LST_PathEnd' lst_stree.c: In function 'stree_get_skipstring': lst_stree.c:468: error: 'end' undeclared (first use in this function) lst_stree.c:476: error: 'skipstring' undeclared (first use in this function) lst_stree.c:488: error: 'tree' undeclared (first use in this function) lst_stree.c:509: error: dereferencing pointer to incomplete type lst_stree.c:531: error: dereferencing pointer to incomplete type lst_stree.c: At top level: lst_stree.c:551: error: syntax error before 'LST_PathEnd' lst_stree.c: In function 'stree_extend_at_node': lst_stree.c:556: error: 'end' undeclared (first use in this function) lst_stree.c:565: error: 'string' undeclared (first use in this function) lst_stree.c:565: error: 'extend_index' undeclared (first use in this function) lst_stree.c:572: error: 'tree' undeclared (first use in this function) lst_stree.c:583: error: 'stop_extensions' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:605: error: syntax error before 'LST_PathEnd' lst_stree.c: In function 'stree_extend_at_edge': lst_stree.c:610: error: 'string' undeclared (first use in this function) lst_stree.c:610: error: 'extend_index' undeclared (first use in this function) lst_stree.c:611: error: 'end' undeclared (first use in this function) lst_stree.c:616: error: 'stop_extensions' undeclared (first use in this function) lst_stree.c:633: error: 'u_int' undeclared (first use in this function) lst_stree.c:637: error: 'tree' undeclared (first use in this function) lst_stree.c:656: error: dereferencing pointer to incomplete type lst_stree.c: In function 'stree_next_phase': lst_stree.c:690: error: invalid application of 'sizeof' to incomplete type 'struct lst_phase_num' lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:692: error: dereferencing pointer to incomplete type lst_stree.c:692: error: dereferencing pointer to incomplete type lst_stree.c: In function 'stree_add_string_impl': lst_stree.c:710: error: syntax error before 'end' lst_stree.c:714: error: storage size of 'skipstring' isn't known lst_stree.c:715: error: 'u_int' undeclared (first use in this function) lst_stree.c:715: error: syntax error before 'i' lst_stree.c:730: error: dereferencing pointer to incomplete type lst_stree.c:735: error: dereferencing pointer to incomplete type lst_stree.c:743: error: 'end' undeclared (first use in this function) lst_stree.c:743: error: dereferencing pointer to incomplete type lst_stree.c:744: error: 'last_extension' undeclared (first use in this function) lst_stree.c:748: error: 'i' undeclared (first use in this function) lst_stree.c:756: error: dereferencing pointer to incomplete type lst_stree.c:758: error: 'find_skipstring' undeclared (first use in this function) lst_stree.c:772: error: dereferencing pointer to incomplete type lst_stree.c:777: error: dereferencing pointer to incomplete type lst_stree.c:779: error: 'use_end' undeclared (first use in this function) lst_stree.c:781: error: 'stop_extensions' undeclared (first use in this function) lst_stree.c:789: error: 'j' undeclared (first use in this function) lst_stree.c:791: error: dereferencing pointer to incomplete type lst_stree.c:810: error: dereferencing pointer to incomplete type lst_stree.c:879: error: dereferencing pointer to incomplete type lst_stree.c:891: error: dereferencing pointer to incomplete type lst_stree.c:892: error: dereferencing pointer to incomplete type lst_stree.c:714: warning: unused variable 'skipstring' lst_stree.c: In function 'lst_stree_add_string': lst_stree.c:901: error: syntax error before 'end' lst_stree.c:902: error: 'u_int' undeclared (first use in this function) lst_stree.c:907: error: dereferencing pointer to incomplete type lst_stree.c:909: error: 'items_done' undeclared (first use in this function) lst_stree.c:909: error: dereferencing pointer to incomplete type lst_stree.c:909: error: 'end' undeclared (first use in this function) lst_stree.c:910: error: dereferencing pointer to incomplete type lst_stree.c:915: error: dereferencing pointer to incomplete type lst_stree.c:915: error: dereferencing pointer to incomplete type lst_stree.c:917: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_new': lst_stree.c:930: error: invalid application of 'sizeof' to incomplete type 'LST_STree' lst_stree.c:946: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_init': lst_stree.c:973: error: invalid application of 'sizeof' to incomplete type 'LST_STree' lst_stree.c:975: error: dereferencing pointer to incomplete type lst_stree.c:976: error: dereferencing pointer to incomplete type lst_stree.c:977: error: dereferencing pointer to incomplete type lst_stree.c:979: error: dereferencing pointer to incomplete type lst_stree.c:980: error: dereferencing pointer to incomplete type lst_stree.c:983: error: dereferencing pointer to incomplete type lst_stree.c:984: error: dereferencing pointer to incomplete type lst_stree.c:988: error: dereferencing pointer to incomplete type lst_stree.c:994: error: dereferencing pointer to incomplete type lst_stree.c:995: error: dereferencing pointer to incomplete type lst_stree.c:997: error: dereferencing pointer to incomplete type lst_stree.c:998: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_clear': lst_stree.c:1013: error: dereferencing pointer to incomplete type lst_stree.c:1016: error: dereferencing pointer to incomplete type lst_stree.c:1018: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1026: error: dereferencing pointer to incomplete type lst_stree.c:1036: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_allow_duplicates': lst_stree.c:1047: error: dereferencing pointer to incomplete type lst_stree.c: In function 'fix_tree_cb': lst_stree.c:1071: error: dereferencing pointer to incomplete type lst_stree.c:1080: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_strMaking install in src if /bin/sh ../libtool --mode=compile --tag=CC gcc -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 ee.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1086: error: dereferencing pointer to incomplete type lst_stree.c:1087: error: dereferencing pointer to incomplete type lst_stree.c:1093: error: dereferencing pointer to incomplete type lst_stree.c:1094: error: dereferencing pointer to incomplete type lst_stree.c:1094: error: dereferencing pointer to incomplete type lst_stree.c:1095: error: dereferencing pointer to incomplete type lst_stree.c:1095: error: dereferencing pointer to incomplete type lst_stree.c:1096: error: dereferencing pointer to incomplete type lst_stree.c:1096: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_remove_string': lst_stree.c:1116: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1138: error: dereferencing pointer to incomplete type lst_stree.c:1142: error: dereferencing pointer to incomplete type lst_stree.c:1144: error: dereferencing pointer to incomplete type lst_stree.c:1152: error: dereferencing pointer to incomplete type lst_stree.c:1153: error: dereferencing pointer to incomplete type lst_stree.c:1159: error: dereferencing pointer to incomplete type lst_stree.c:1160: error: dereferencing pointer to incomplete type lst_stree.c:1160: error: dereferencing pointer to incomplete type lst_stree.c:1160: error: dereferencing pointer to incomplete type lst_stree.c:1169: error: dereferencing pointer to incomplete type lst_stree.c:1170: error: dereferencing pointer to incomplete type lst_stree.c:1192: error: dereferencing pointer to incomplete type lst_stree.c:1194: error: dereferencing pointer to incomplete type lst_stree.c:1194: error: dereferencing pointer to incomplete type lst_stree.c:1197: error: dereferencing pointer to incomplete type lst_stree.c:1197: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_get_string_index': lst_stree.c:1216: error: dereferencing pointer to incomplete type lst_stree.c:1216: error: dereferencing pointer to incomplete type lst_stree.c:1220: error: dereferencing pointer to incomplete type lst_stree.c:1220: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_get_parent': lst_stree.c:1231: error: dereferencing pointer to incomplete type lst_stree.c:1234: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_is_leaf': lst_stree.c:1244: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_is_root': lst_stree.c:1254: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_get_string_length': lst_stree.c:1268: error: dereferencing pointer to incomplete type lst_stree.c:1269: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_get_string': lst_stree.c:1288: error: dereferencing pointer to incomplete type lst_stree.c:1289: error: dereferencing pointer to incomplete type lst_stree.c:1289: error: dereferencing pointer to incomplete type lst_stree.c:1293: error: dereferencing pointer to incomplete type lst_stree.c:1298: error: dereferencing pointer to incomplete type lst_stree.c:1299: error: dereferencing pointer to incomplete type lst_stree.c:1301: error: dereferencing pointer to incomplete type lst_stree.c:1306: error: dereferencing pointer to incomplete type lst_stree.c:1306: error: dereferencing pointer to incomplete type lst_stree.c:1318: error: dereferencing pointer to incomplete type make[2]: *** [lst_stree.lo] Error 1 make[1]: *** [all-recursive] Error 1 make: *** [all] Error 2 gcc -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 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: syntax error before 'u_char' lst_string.h:101: warning: no semicolon at end of struct or union lst_string.h:103: warning: type defaults to 'int' in declaration of 'num_items' lst_string.h:103: warning: data definition has no type or storage class lst_string.h:104: error: syntax error before 'item_size' lst_string.h:104: warning: type defaults to 'int' in declaration of 'item_size' lst_string.h:104: warning: data definition has no type or storage class lst_string.h:107: error: syntax error before '}' token lst_string.h:130: error: syntax error before 'u_int' lst_string.h:130: warning: no semicolon at end of struct or union lst_string.h:136: warning: type defaults to 'int' in declaration of 'end_index' lst_string.h:136: warning: data definition has no type or storage class lst_string.h:137: error: syntax error before 'end_index_local' lst_string.h:137: warning: type defaults to 'int' in declaration of 'end_index_local' lst_string.h:137: warning: data definition has no type or storage class lst_string.h:143: error: syntax error before 'extra_index' lst_string.h:143: warning: type defaults to 'int' in declaration of 'extra_index' lst_string.h:143: warning: data definition has no type or storage class lst_string.h:165: error: syntax error before 'u_int' lst_string.h:180: error: syntax error before 'u_int' lst_string.h:217: error: syntax error before 'lst_string_get_length' lst_string.h:217: warning: type defaults to 'int' in declaration of 'lst_string_get_length' lst_string.h:217: warning: data definition has no type or storage class lst_string.h:228: error: syntax error before 'u_int' lst_string.h:254: error: syntax error before 'u_int' lst_string.h:271: error: syntax error before 'u_int' lst_string.h:289: error: syntax error before 'lst_string_items_common' lst_string.h:289: error: syntax error before 'u_int' lst_string.h:291: warning: type defaults to 'int' in declaration of 'lst_string_items_common' lst_string.h:291: warning: data definition has no type or storage class In file included from lst_stree.h:34, from lst_stree.c:34: lst_structs.h:47: error: field 'range' has incomplete type lst_structs.h:55: error: syntax error before 'u_int' lst_structs.h:55: warning: no semicolon at end of struct or union lst_structs.h:67: error: 'index' redeclared as different kind of symbol lst_structs.h:68: error: syntax error before 'id' lst_structs.h:68: warning: type defaults to 'int' in declaration of 'id' lst_structs.h:68: warning: data definition has no type or storage class lst_structs.h:71: error: syntax error before 'bus_visited' lst_structs.h:71: warning: type defaults to 'int' in declaration of 'bus_visited' lst_structs.h:71: warning: data definition has no type or storage class lst_structs.h:79: error: syntax error before 'u_int' lst_structs.h:79: warning: no semicolon at end of struct or union lst_structs.h:96: error: syntax error before 'u_int' lst_structs.h:96: warning: no semicolon at end of struct or union lst_structs.h:103: warning: type defaults to 'int' in declaration of 'phase' lst_structs.h:103: warning: data definition has no type or storage class lst_structs.h:113: error: syntax error before 'ext' lst_structs.h:113: warning: type defaults to 'int' in declaration of 'ext' lst_structs.h:113: warning: data definition has no type or storage class lst_structs.h:119: error: conflicting types for 'leafs' lst_structs.h:61: error: previous declaration of 'leafs' was here lst_structs.h:143: error: syntax error before 'visitors' lst_structs.h:143: warning: type defaults to 'int' in declaration of 'visitors' lst_structs.h:143: error: conflicting types for 'visitors' lst_structs.h:70: error: previous declaration of 'visitors' was here lst_structs.h:143: warning: data definition has no type or storage class In file included from lst_stree.c:36: lst_algorithms.h:107: error: syntax error before 'lst_alg_set_visitors' lst_algorithms.h:107: warning: type defaults to 'int' in declaration of 'lst_alg_set_visitors' lst_algorithms.h:107: warning: data definition has no type or storage class lst_algorithms.h:128: error: syntax error before 'u_int' lst_algorithms.h:149: error: syntax error before 'u_int' lst_stree.c:55: error: syntax error before 'u_int' lst_stree.c:55: warning: no semicolon at end of struct or union lst_stree.c:57: warning: type defaults to 'int' in declaration of 'LST_PathEnd' lst_stree.c:57: warning: data definition has no type or storage class lst_stree.c:64: error: syntax error before 'u_int' lst_stree.c: In function 'edge_new': lst_stree.c:76: error: 'src_node' undeclared (first use in this function) lst_stree.c:76: error: (Each undeclared identifier is reported only once lst_stree.c:76: error: for each function it appears in.) lst_stree.c:77: error: 'dst_node' undeclared (first use in this function) lst_stree.c:79: error: 'string' undeclared (first use in this function) lst_stree.c:80: error: 'start_index' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:98: error: syntax error before 'u_int' lst_stree.c: In function 'edge_leaf_new': lst_stree.c:100: error: 'src_node' undeclared (first use in this function) lst_stree.c:100: error: 'dst_node' undeclared (first use in this function) lst_stree.c:100: error: 'string' undeclared (first use in this function) lst_stree.c:100: error: 'start_index' undeclared (first use in this function) lst_stree.c:108: error: 'tree' undeclared (first use in this function) lst_stree.c: In function 'node_new': lst_stree.c:129: error: nested functions are disabled, use -fnested- functions to re-enable lst_stree.c:129: error: syntax error before 'id' lst_stree.c:132: error: invalid application of 'sizeof' to incomplete type 'LST_Node' lst_stree.c:140: error: dereferencing pointer to incomplete type lst_stree.c:141: error: dereferencing pointer to incomplete type lst_stree.c:142: error: dereferencing pointer to incomplete type lst_stree.c: In function 'node_free': lst_stree.c:156: error: dereferencing pointer to incomplete type lst_stree.c:156: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:157: error: dereferencing pointer to incomplete type lst_stree.c:160: error: dereferencing pointer to incomplete type lst_stree.c:162: error: dereferencing pointer to incomplete type lst_stree.c:163: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c:164: error: dereferencing pointer to incomplete type lst_stree.c: At top level: lst_stree.c:172: error: syntax error before 'u_int' lst_stree.c: In function 'node_find_edge_with_startitem': lst_stree.c:176: error: 'node' undeclared (first use in this function) lst_stree.c:176: error: 'string' undeclared (first use in this function) lst_stree.c: In function 'stree_remove_edge': lst_stree.c:206: error: dereferencing pointer to incomplete type lst_stree.c:209: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c:210: error: dereferencing pointer to incomplete type lst_stree.c: In function 'stree_extend_label_at_leaf': lst_stree.c:222: error: dereferencing pointer to incomplete type lst_stree.c:222: error: dereferencing pointer to incomplete type lst_stree.c: At top level: lst_stree.c:227: error: syntax error before '*' token lst_stree.c: In function 'stree_path_end_node': lst_stree.c:229: error: 'end' undeclared (first use in this function) lst_stree.c:230: error: 'node' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:235: error: syntax error before '*' token lst_stree.c: In function 'stree_path_end_edge': lst_stree.c:237: error: 'end' undeclared (first use in this function) lst_stree.c:238: error: 'edge' undeclared (first use in this function) lst_stree.c:239: error: 'offset' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:244: error: syntax error before '*' token lst_stree.c: In function 'stree_path_end_advance': lst_stree.c:246: error: 'end' undeclared (first use in this function) lst_stree.c:251: error: 'edge' undeclared (first use in this function) lst_stree.c:260: error: 'u_int' undeclared (first use in this function) lst_stree.c:260: error: syntax error before 'lst_edge_get_length' lst_stree.c: At top level: lst_stree.c:280: error: syntax error before 'stree_follow_string_slow' lst_stree.c:281: error: syntax error before 'LST_PathEnd' lst_stree.c:282: warning: return type defaults to 'int' lst_stree.c: In function 'stree_follow_string_slow': lst_stree.c:284: error: 'u_int' undeclared (first use in this function) lst_stree.c:284: error: syntax error before 'items_todo' lst_stree.c:286: error: 'tree' undeclared (first use in this function) lst_stree.c:286: error: 'node' undeclared (first use in this function) lst_stree.c:286: error: 'string' undeclared (first use in this function) lst_stree.c:286: error: 'end' undeclared (first use in this function) lst_stree.c:293: error: 'items_todo' undeclared (first use in this function) lst_stree.c:301: error: 'items_done' undeclared (first use in this function) lst_stree.c:311: error: 'common' undeclared (first use in this function) lst_stree.c:316: error: syntax error before 'lst_edge_get_length' lst_stree.c: At top level: lst_stree.c:329: warning: type defaults to 'int' in declaration of 'stree_path_end_node' lst_stree.c:329: warning: parameter names (without types) in function declaration lst_stree.c:329: error: conflicting types for 'stree_path_end_node' lst_stree.c:228: error: previous definition of 'stree_path_end_node' was here lst_stree.c:329: warning: data definition has no type or storage class lst_stree.c:330: error: syntax error before 'return' lst_stree.c:347: error: syntax error before 'LST_PathEnd' lst_stree.c: In function 'stree_follow_string': lst_stree.c:351: error: 'u_int' undeclared (first use in this function) lst_stree.c:351: error: syntax error before 'items_todo' lst_stree.c:353: error: 'tree' undeclared (first use in this function) lst_stree.c:353: error: 'node' undeclared (first use in this function) lst_stree.c:353: error: 'skipstring' undeclared (first use in this function) lst_stree.c:353: error: 'end' undeclared (first use in this function) lst_stree.c:376: error: 'items_todo' undeclared (first use in this function) lst_stree.c:391: error: syntax error before 'edge_len' lst_stree.c:393: error: 'items_done' undeclared (first use in this function) lst_stree.c:401: error: 'edge_len' undeclared (first use in this function) lst_stree.c:401: error: syntax error before 'lst_edge_get_length' lst_stree.c:435: error: 'common' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:464: error: syntax error before 'LST_PathEnd' lst_stree.c: In function 'stree_get_skipstring': lst_stree.c:468: error: 'end' undeclared (first use in this function) lst_stree.c:476: error: 'skipstring' undeclared (first use in this function) lst_stree.c:488: error: 'tree' undeclared (first use in this function) lst_stree.c:509: error: dereferencing pointer to incomplete type lst_stree.c:531: error: dereferencing pointer to incomplete type lst_stree.c: At top level: lst_stree.c:551: error: syntax error before 'LST_PathEnd' lst_stree.c: In function 'stree_extend_at_node': lst_stree.c:556: error: 'end' undeclared (first use in this function) lst_stree.c:565: error: 'string' undeclared (first use in this function) lst_stree.c:565: error: 'extend_index' undeclared (first use in this function) lst_stree.c:572: error: 'tree' undeclared (first use in this function) lst_stree.c:583: error: 'stop_extensions' undeclared (first use in this function) lst_stree.c: At top level: lst_stree.c:605: error: syntax error before 'LST_PathEnd' lst_stree.c: In function 'stree_extend_at_edge': lst_stree.c:610: error: 'string' undeclared (first use in this function) lst_stree.c:610: error: 'extend_index' undeclared (first use in this function) lst_stree.c:611: error: 'end' undeclared (first use in this function) lst_stree.c:616: error: 'stop_extensions' undeclared (first use in this function) lst_stree.c:633: error: 'u_int' undeclared (first use in this function) lst_stree.c:637: error: 'tree' undeclared (first use in this function) lst_stree.c:656: error: dereferencing pointer to incomplete type lst_stree.c: In function 'stree_next_phase': lst_stree.c:690: error: invalid application of 'sizeof' to incomplete type 'struct lst_phase_num' lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:691: error: dereferencing pointer to incomplete type lst_stree.c:692: error: dereferencing pointer to incomplete type lst_stree.c:692: error: dereferencing pointer to incomplete type lst_stree.c: In function 'stree_add_string_impl': lst_stree.c:710: error: syntax error before 'end' lst_stree.c:714: error: storage size of 'skipstring' isn't known lst_stree.c:715: error: 'u_int' undeclared (first use in this function) lst_stree.c:715: error: syntax error before 'i' lst_stree.c:730: error: dereferencing pointer to incomplete type lst_stree.c:735: error: dereferencing pointer to incomplete type lst_stree.c:743: error: 'end' undeclared (first use in this function) lst_stree.c:743: error: dereferencing pointer to incomplete type lst_stree.c:744: error: 'last_extension' undeclared (first use in this function) lst_stree.c:748: error: 'i' undeclared (first use in this function) lst_stree.c:756: error: dereferencing pointer to incomplete type lst_stree.c:758: error: 'find_skipstring' undeclared (first use in this function) lst_stree.c:772: error: dereferencing pointer to incomplete type lst_stree.c:777: error: dereferencing pointer to incomplete type lst_stree.c:779: error: 'use_end' undeclared (first use in this function) lst_stree.c:781: error: 'stop_extensions' undeclared (first use in this function) lst_stree.c:789: error: 'j' undeclared (first use in this function) lst_stree.c:791: error: dereferencing pointer to incomplete type lst_stree.c:810: error: dereferencing pointer to incomplete type lst_stree.c:879: error: dereferencing pointer to incomplete type lst_stree.c:891: error: dereferencing pointer to incomplete type lst_stree.c:892: error: dereferencing pointer to incomplete type lst_stree.c:714: warning: unused variable 'skipstring' lst_stree.c: In function 'lst_stree_add_string': lst_stree.c:901: error: syntax error before 'end' lst_stree.c:902: error: 'u_int' undeclared (first use in this function) lst_stree.c:907: error: dereferencing pointer to incomplete type lst_stree.c:909: error: 'items_done' undeclared (first use in this function) lst_stree.c:909: error: dereferencing pointer to incomplete type lst_stree.c:909: error: 'end' undeclared (first use in this function) lst_stree.c:910: error: dereferencing pointer to incomplete type lst_stree.c:915: error: dereferencing pointer to incomplete type lst_stree.c:915: error: dereferencing pointer to incomplete type lst_stree.c:917: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_new': lst_stree.c:930: error: invalid application of 'sizeof' to incomplete type 'LST_STree' lst_stree.c:946: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_init': lst_stree.c:973: error: invalid application of 'sizeof' to incomplete type 'LST_STree' lst_stree.c:975: error: dereferencing pointer to incomplete type lchecking for gcc... gcc st_stree.c:976: error: dereferencing pointer to incomplete type lst_stree.c:977: error: dereferencing pointer to incomplete type lst_stree.c:979: error: dereferencing pointer to incomplete type lst_stree.c:980: error: dereferencing pointer to incomplete type lst_stree.c:983: error: dereferencing pointer to incomplete type lst_stree.c:984: error: dereferencing pointer to incomplete type lst_stree.c:988: error: dereferencing pointer to incomplete type lst_stree.c:994: error: dereferencing pointer to incomplete type lst_stree.c:995: error: dereferencing pointer to incomplete type lst_stree.c:997: error: dereferencing pointer to incomplete type lst_stree.c:998: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_clear': lst_stree.c:1013: error: dereferencing pointer to incomplete type lst_stree.c:1016: error: dereferencing pointer to incomplete type lst_stree.c:1018: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1019: error: dereferencing pointer to incomplete type lst_stree.c:1026: error: dereferencing pointer to incomplete type lst_stree.c:1036: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_allow_duplicates': lst_stree.c:1047: error: dereferencing pointer to incomplete type lst_stree.c: In function 'fix_tree_cb': lst_stree.c:1071: error: dereferencing pointer to incomplete type lst_stree.c:1080: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1082: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1083: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1084: error: dereferencing pointer to incomplete type lst_stree.c:1086: error: dereferencing pointer to incomplete type lst_stree.c:1087: error: dereferencing pointer to incomplete type lst_stree.c:1093: error: dereferencing pointer to incomplete type lst_stree.c:1094: error: dereferencing pointer to incomplete type lst_stree.c:1094: error: dereferencing pointer to incomplete type lst_stree.c:1095: error: dereferencing pointer to incomplete type lst_stree.c:1095: error: dereferencing pointer to incomplete type lst_stree.c:1096: error: dereferencing pointer to incomplete type lst_stree.c:1096: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_remove_string': lst_stree.c:1116: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1127: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: errorchecking for C compiler default output file name... : dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1132: error: dereferencing pointer to incomplete type lst_stree.c:1138: error: dereferencing pointer to incomplete type lst_stree.c:1142: error: dereferencing pointer to incomplete type lst_stree.c:1144: error: dereferencing pointer to incomplete type lst_stree.c:1152: error: dereferencing pointer to incomplete type lst_stree.c:1153: error: dereferencing pointer to incomplete type lst_stree.c:1159: error: dereferencing pointer to incomplete type lst_stree.c:1160: error: dereferencing pointer to incomplete type lst_stree.c:1160: error: dereferencing pointer to incomplete type lst_stree.c:1160: error: dereferencing pointer to incomplete type lst_stree.c:1169: error: dereferencing pointer to incomplete type lst_stree.c:1170: error: dereferencing pointer to incomplete type lst_stree.c:1192: error: dereferencing pointer to incomplete type lst_stree.c:1194: error: dereferencing pointer to incomplete type lst_stree.c:1194: error: dereferencing pointer to incomplete type lst_stree.c:1197: error: dereferencing pointer to incomplete type lst_stree.c:1197: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_stree_get_string_index': lst_stree.c:1216: error: dereferencing pointer to incomplete type lst_stree.c:1216: error: dereferencing pointer to incomplete type lst_stree.c:1220: error: dereferencing pointer to incomplete type lst_stree.c:1220: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_get_parent': lst_stree.c:1231: error: dereferencing pointer to incomplete type lst_stree.c:1234: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_is_leaf': lst_stree.c:1244: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_is_root': lst_stree.c:1254: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_get_string_length': lst_stree.c:1268: error: dereferencing pointer to incomplete type lst_stree.c:1269: error: dereferencing pointer to incomplete type lst_stree.c: In function 'lst_node_get_string': lst_stree.c:1288: error: dereferencing pointer to incomplete type lst_stree.c:1289: error: dereferencing pointer to incomplete type lst_stree.c:1289: error: dereferencing pointer to incomplete type lst_stree.c:1293: error: dereferencing pointer to incomplete type lst_stree.c:1298: error: dereferencing pointer to incomplete type lst_stree.c:1299: error: dereferencing pointer to incomplete type lst_stree.c:1301: error: dereferencing pointer to incomplete type lst_stree.c:1306: error: dereferencing pointer to incomplete type lst_stree.c:1306: error: dereferencing pointer to incomplete type lst_stree.c:1318: error: dereferencing pointer to incomplete type make[1]: *** [lst_stree.lo] Error 1 make: *** [install-recursive] Error 1 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 checking for egrep... grep -E checking for ANSI C header files... yes checking for sys/types.h... yes checking for sys/stat.h... yes checking for stdlib.h... yes checking for string.h... yes checking for memory.h... yes checking for strings.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for unistd.h... yes checking stree/lst_structs.h usability... yes checking stree/lst_structs.h presence... yes checking for stree/lst_structs.h... yes configure: creating ./config.status config.status: creating src/Makevars Building Rlibstree ** libs ** arch - ppc gcc-4.2 -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-4.2 -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-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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 ld: warning in /usr/local/lib/libstree.so, file is not of required architecture ** R ** inst ** preparing package for lazy loading Creating a new generic function for "lapply" in "Rlibstree" Creating a new generic function for "sapply" in "Rlibstree" Creating a new generic function for "append" in "Rlibstree" ** help >>> Building/Updating help pages for package 'Rlibstree' Formats: text html latex example StringSet-class text html latex example StringSet text html latex example SuffixTree-class text html latex example SuffixTree-methods text html latex append-methods text html latex getCommonPrefix text html latex example getLongestSubstring text html latex example lapply-methods text html latex ** building package indices ... * DONE (Rlibstree) The downloaded packages are in /private/var/folders/4q/4qrd+OVfHLOrqZ6iI1mrA++++TI/-Tmp-/Rtmp qocqcY/downloaded_packages >