Loading problem with Rlibstree and microRNA packages on MacOS X 10.4

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Steven McKinney ▴ 310

@steven-mckinney-1754

Last seen 9.7 years ago

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@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/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 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/li brary/Rlibstree' ** Restoring previous '/Library/Frameworks/R.framework/Versions/2.8/Re sources/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

Cancer Breast rtracklayer microRNA Cancer Breast rtracklayer microRNA • 1.3k views

ADD COMMENT • link updated 15.4 years ago by Luo Weijun ★ 1.6k • written 15.4 years ago by Steven McKinney ▴ 310

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Entering edit mode

Luo Weijun ★ 1.6k

@luo-weijun-1783

Last seen 10 months ago

United States

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

ADD COMMENT • link 15.4 years ago Luo Weijun ★ 1.6k

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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/p pc/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/pp c/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/Rlib stree/libs/ppc/*: >> No such file or directory >> ERROR: compilation failed for package 'Rlibstree' >> ** Removing >> '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Rli bstree' >> ** Restoring previous >> '/Library/Frameworks/R.framework/Versions/2.8/Resources/library/Rli bstree' >> >> >> >> >> >> _______________________________________________ >> 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

ADD REPLY • link 15.4 years ago Duncan Temple Lang ▴ 110

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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

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