Dear All, I have this problem with R-2.7.0 when loading RCurl on a 64 bit machine. I am using a ubuntu 8.04. > library(RCurl) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/home/john/R/x86_64-unknown-linux-gnu- library/2.7/RCurl/libs/RCurl.so': /home/john/R/x86_64-unknown-linux-gnu- library/2.7/RCurl/libs/RCurl.so: undefined symbol: Curl_base64_encode Error: package/namespace load failed for 'RCurl' what can i do? best > session sessionData sessionInfo > sessionInfo() R version 2.7.0 (2008-04-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base [[alternative HTML version deleted]]

I am having a similar problem with RCurl after R2.7.0 although it does not appear to be 64-bit-related... On Mac OS X 10.5... > library(RCurl) Error in dyn.load(file, DLLpath = DLLpath, ...) : unable to load shared library '/Library/Frameworks/R.framework/ Resources/library/RCurl/libs/i386/RCurl.so': dlopen(/Library/Frameworks/R.framework/Resources/library/RCurl/libs/ i386/RCurl.so, 6): Library not loaded: /Library/Frameworks/R.framework/ Versions/2.6/Resources/lib/libR.dylib Referenced from: /Library/Frameworks/R.framework/Resources/library/ RCurl/libs/i386/RCurl.so Reason: image not found Error: package/namespace load failed for 'RCurl' > sessionInfo() R version 2.7.0 (2008-04-22) i386-apple-darwin8.10.1 locale: en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base On May 6, 2008, at 5:48 AM, John Lande wrote: > Dear All, > I have this problem with R-2.7.0 when loading RCurl on a 64 bit > machine. > I am using a ubuntu 8.04. > >> library(RCurl) > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library > '/home/john/R/x86_64-unknown-linux-gnu-library/2.7/RCurl/libs/ > RCurl.so': > /home/john/R/x86_64-unknown-linux-gnu-library/2.7/RCurl/libs/ > RCurl.so: > undefined symbol: Curl_base64_encode > Error: package/namespace load failed for 'RCurl' > > what can i do? > > best > >> session > sessionData sessionInfo >> sessionInfo() > R version 2.7.0 (2008-04-22) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE > = > en_US > .UTF > -8 > ;LC_NUMERIC > = > C > ;LC_TIME > = > en_US > .UTF > -8 > ;LC_COLLATE > = > en_US > .UTF > -8 > ;LC_MONETARY > = > C > ;LC_MESSAGES > = > en_US > .UTF > -8 > ;LC_PAPER > = > en_US > .UTF > -8 > ;LC_NAME > = > C > ;LC_ADDRESS > =C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Loyal A. Goff, Ph.D., Rutgers Stem Cell Research Center Rutgers: The State University of New Jersey Nelson Biology Labs D-251 604 Allison Rd, Piscataway, NJ 08854 lgoff at rci.rutgers.edu

Hi Mark... A couple of shots in the dark, as no one else seems to be leaping in... The symbol Curl_base64_encode should be defined in /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so. What does nm /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so say? Mine says 0000000000003980 T Curl_base64_encode with the 'T' indicating that the symbol is defined (make sure nm spits out a bunch of lines before concluding that Curl_base64_encode is not defined). I retrieved the RCurl source, and one thing I notice is that RCurl/src/curl_base64.c has the 'execute' bit set, and perhaps a sane system would not compile it. Try % chmod -x RCurl/src/curl_base64.c and then % R CMD INSTALL RCurl Martin "Mark Kimpel" <mwkimpel at="" gmail.com=""> writes: > I'm having same problem on Ubuntu 64-bit Hardy Heron. A bunch of security > patches from Ubuntu came out and I installed them today. After that was when > I first noted the problem (affycoretools, which I use all the time, won't > load). Below is my initial output, what follows is my reinstallation output > followed by the same error messages as obtained intially. I wonder if a > security patch has changed Curl? Or did RCurl just change? I have been using > R-2.7.0 since half-way through its develoment cycle and this is a new > problem for me. > > Mark > >> require(RCurl) > Loading required package: RCurl > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library > '/home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so': > /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so: undefined > symbol: Curl_base64_encode >> install.packages("RCurl") > >> sessionInfo() > R version 2.7.0 Patched (2008-05-04 r45620) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] graph_1.18.0 > > loaded via a namespace (and not attached): > [1] cluster_1.11.10 tcltk_2.7.0 tools_2.7.0 >> > > mkimpel-m90 ~: R CMD INSTALL ~/Desktop/RCurl_0.9-1.tar.gz > Loading required package: methods > Loading required package: datasets > Loading required package: utils > Loading required package: grDevices > Loading required package: graphics > Loading required package: stats > Loading required package: graph > * Installing to library '/home/mkimpel/R_HOME/site-library-2.7.0' > * Installing *source* package 'RCurl' ... > checking for curl-config... /usr/bin/curl-config > 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 how to run the C preprocessor... gcc -E > Version has a libidn field > Using Curl_base64_encode with SessionHandle parameter. > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include > -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/usr/local/include > -fpic -g -O2 -c base64.c -o base64.o > base64.c: In function 'R_base64_decode': > base64.c:27: warning: implicit declaration of function 'Curl_base64_decode' > base64.c: In function 'R_base64_encode': > base64.c:64: warning: implicit declaration of function 'Curl_base64_encode' > gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include > -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/usr/local/include > -fpic -g -O2 -c curl_base64.c -o curl_base64.o > gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include > -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/usr/local/include > -fpic -g -O2 -c curl.c -o curl.o > curl.c: In function 'getRStringsFromNullArray': > curl.c:1104: warning: assignment discards qualifiers from pointer target > type > curl.c:1107: warning: assignment discards qualifiers from pointer target > type > gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include > -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/usr/local/include > -fpic -g -O2 -c curlInit.c -o curlInit.o > gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include > -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/usr/local/include > -fpic -g -O2 -c enums.c -o enums.o > gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include > -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/usr/local/include > -fpic -g -O2 -c memoryManagement.c -o memoryManagement.o > memoryManagement.c: In function 'RCurl_releaseManagerMemoryTickets': > memoryManagement.c:143: warning: passing argument 1 of 'free' discards > qualifiers from pointer target type > gcc -std=gnu99 -shared -L/usr/local/lib64 -o RCurl.so base64.o curl_base64.o > curl.o curlInit.o enums.o memoryManagement.o -lcurl -lgssapi_krb5 > ** R > ** inst > ** preparing package for lazy loading > ** help > >>> Building/Updating help pages for package 'RCurl' > Formats: text html latex example > Note: removing empty section \examples > CURLHandle-class text html latex > Note: removing empty section \references > Note: removing empty section \seealso > Note: removing empty section \examples > CurlFeatureBits text html latex > Note: unmatched right brace in file 'MultiCURLHandle-class.Rd' on or after > line 28 > Note: removing empty section \examples > MultiCURLHandle-class text html latex > RCurl-internal text html latex > Note: removing empty section \seealso > base64 text html latex example > basicHeaderGatherer text html latex example > basicTextGatherer text html latex example > Note: removing empty section \details > binaryBuffer text html latex example > chunkToLineReader text html latex example > Note: removing empty section \value > complete text html latex example > curlEscape text html latex example > curlGlobalInit text html latex example > curlOptions text html latex example > Note: unmatched right brace in file 'curlPerform.Rd' on or after line 18 > Note: removing empty section \details > curlPerform text html latex example > Note: removing empty section \examples > curlSetOpt text html latex > Note: removing empty section \details > curlVersion text html latex example > Note: removing empty section \examples > fileUpload text html latex > findHTTPHeaderEncoding text html latex example > getBitIndicators text html latex example > Note: removing empty section \examples > getCurlHandle text html latex > getCurlInfo text html latex example > getURIAsynchronous text html latex example > Note: removing empty section \details > getURL text html latex example > merge.list text html latex example > postForm text html latex example > ** building package indices ... > * DONE (RCurl) > mkimpel-m90 ~: R > > R version 2.7.0 Patched (2008-05-04 r45620) > Copyright (C) 2008 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Loading required package: datasets > Loading required package: utils > Loading required package: grDevices > Loading required package: graphics > Loading required package: stats > Loading required package: graph > [1] "packages do not need updated" >> require(RCurl) > Loading required package: RCurl > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library > '/home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so': > /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so: undefined > symbol: Curl_base64_encode >> > > > > On Tue, May 6, 2008 at 7:49 AM, Loyal Goff <lgoff at="" rci.rutgers.edu=""> wrote: > >> I am having a similar problem with RCurl after R2.7.0 although it does not >> appear to be 64-bit-related... >> >> On Mac OS X 10.5... >> >> > library(RCurl) >> Error in dyn.load(file, DLLpath = DLLpath, ...) : >> unable to load shared library >> '/Library/Frameworks/R.framework/Resources/library/RCurl/libs/i386/ RCurl.so': >> dlopen(/Library/Frameworks/R.framework/Resources/library/RCurl/lib s/i386/RCurl.so, >> 6): Library not loaded: >> /Library/Frameworks/R.framework/Versions/2.6/Resources/lib/libR.dylib >> Referenced from: >> /Library/Frameworks/R.framework/Resources/library/RCurl/libs/i386/R Curl.so >> Reason: image not found >> Error: package/namespace load failed for 'RCurl' >> >> > sessionInfo() >> R version 2.7.0 (2008-04-22) >> i386-apple-darwin8.10.1 >> >> locale: >> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> >> >> On May 6, 2008, at 5:48 AM, John Lande wrote: >> >> Dear All, >> > I have this problem with R-2.7.0 when loading RCurl on a 64 bit machine. >> > I am using a ubuntu 8.04. >> > >> > library(RCurl) >> > > >> > Error in dyn.load(file, DLLpath = DLLpath, ...) : >> > unable to load shared library >> > '/home/john/R/x86_64-unknown-linux-gnu- library/2.7/RCurl/libs/RCurl.so': >> > /home/john/R/x86_64-unknown-linux-gnu- library/2.7/RCurl/libs/RCurl.so: >> > undefined symbol: Curl_base64_encode >> > Error: package/namespace load failed for 'RCurl' >> > >> > what can i do? >> > >> > best >> > >> > session >> > > >> > sessionData sessionInfo >> > >> > > sessionInfo() >> > > >> > R version 2.7.0 (2008-04-22) >> > x86_64-unknown-linux-gnu >> > >> > locale: >> > >> > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8 ;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_I DENTIFICATION=C >> > >> > attached base packages: >> > [1] stats graphics grDevices utils datasets methods base >> > >> > [[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > 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 >> > >> >> Loyal A. Goff, Ph.D., >> >> Rutgers Stem Cell Research Center >> Rutgers: The State University of New Jersey >> Nelson Biology Labs D-251 >> 604 Allison Rd, >> Piscataway, NJ 08854 >> lgoff at rci.rutgers.edu >> >> >> _______________________________________________ >> 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 >> > > > > -- > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793

Hi Joern et al., This thread seems to have migrated to the R-devel mailing list, where the currently definitive answer seems to be, from Prof. Ripley, > If you can, I'd wait until that is resolved. I have installed > RCurl_0.8-3 for production' use. (It is still up at > http://www.omegahat.org/RCurl/RCurl_0.8-3.tar.gz, Martin Joern Toedling <toedling at="" ebi.ac.uk=""> writes: > Hello, > unfortunately I cannot provide a solution, but maybe I can give some more details that may help to > pinpoint the source of the problem. > I get exactly the same error message as Mark on R-2.8.0, when trying to install R-Curl_0.9-1 and then attach it: > Indeed, upon using nm to look at RCurl.so, the output > ... > 000000000209420 D CurlOptionNames > U Curl_base64_decode > U Curl_base64_encode > ... > indicates that Curl_base64_encode is not defined. > Removing the execute bit before installation, as Martin suggested, > unfortunately did not solve the problem. Strangely enough, with > R-Curl_0.8-3, it was defined as 0000000000003978 T Curl_base64_encode > but then when trying to attach RCurl I got > >> library("RCurl") > > Error in dyn.load(file, DLLpath = DLLpath, ...) : > > unable to load shared library '/home/toedling/rpackages/RCurl/libs/RCurl.so': > > /home/toedling/rpackages/RCurl/libs/RCurl.so: undefined symbol: allocString > > Looking at the RCurl web page of changes > > http://www.omegahat.org/RCurl/Changes.html > > it seemed that they were aware of the allocString issue and fixed it > in R-0.9-0, but maybe then introduced the Curl_base64_encode issue. > > Any more suggestions on how to fix this would be very welcome. > Below are my sessionInfo and the output upon installing RCurl-0.9-1. > > Cheers, > Joern > >> library("RCurl") > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared library '/home/toedling/rpackages/RCurl/libs/RCurl.so': > /home/toedling/rpackages/RCurl/libs/RCurl.so: undefined symbol: Curl_base64_encode > Error: package/namespace load failed for 'RCurl' >> sessionInfo() > R version 2.8.0 Under development (unstable) (2008-04-21 r45421) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.ISO-8859-1;LC_NUMERIC=C;LC_TIME=en_US.ISO-8859-1;LC_C OLLATE=en_US.ISO-8859-1;LC_MONETARY=C;LC_MESSAGES=en_US.ISO-8859-1;LC_ PAPER=en_US.ISO-8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUR EMENT=en_US.ISO-8859-1;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] fortunes_1.3-3 > > ### R CMD INSTALL RCurl > > * Installing *source* package 'RCurl' ... > checking for curl-config... /usr/bin/curl-config > 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 how to run the C preprocessor... gcc -E > Version has a libidn field > Using Curl_base64_encode with SessionHandle parameter. > configure: creating ./config.status > config.status: creating src/Makevars > ** libs > gcc -std=gnu99 -I/home/toedling/local/R/R-devel/include -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/home/toedling/local/include/graphviz -I/local/include -fpic -I/home/toedling/local/include/graphviz -I/local/include -c base64.c -o base64.o > base64.c: In function 'R_base64_decode': > base64.c:27: warning: implicit declaration of function 'Curl_base64_decode' > base64.c: In function 'R_base64_encode': > base64.c:64: warning: implicit declaration of function 'Curl_base64_encode' > gcc -std=gnu99 -I/home/toedling/local/R/R-devel/include -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/home/toedling/local/include/graphviz -I/local/include -fpic -I/home/toedling/local/include/graphviz -I/local/include -c curl_base64.c -o curl_base64.o > gcc -std=gnu99 -I/home/toedling/local/R/R-devel/include -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/home/toedling/local/include/graphviz -I/local/include -fpic -I/home/toedling/local/include/graphviz -I/local/include -c curl.c -o curl.o > curl.c: In function 'getRStringsFromNullArray': > curl.c:1104: warning: assignment discards qualifiers from pointer target type > curl.c:1107: warning: assignment discards qualifiers from pointer target type > gcc -std=gnu99 -I/home/toedling/local/R/R-devel/include -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/home/toedling/local/include/graphviz -I/local/include -fpic -I/home/toedling/local/include/graphviz -I/local/include -c curlInit.c -o curlInit.o > gcc -std=gnu99 -I/home/toedling/local/R/R-devel/include -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/home/toedling/local/include/graphviz -I/local/include -fpic -I/home/toedling/local/include/graphviz -I/local/include -c enums.c -o enums.o > gcc -std=gnu99 -I/home/toedling/local/R/R-devel/include -DHAVE_LIBIDN_FIELD=1 -DBASE64_NEEDS_SESSION_DATA=1 -I/home/toedling/local/include/graphviz -I/local/include -fpic -I/home/toedling/local/include/graphviz -I/local/include -c memoryManagement.c -o memoryManagement.o > memoryManagement.c: In function 'RCurl_releaseManagerMemoryTickets': > memoryManagement.c:143: warning: passing argument 1 of 'free' discards qualifiers from pointer target type > gcc -std=gnu99 -shared -L/home/toedling/local/lib/graphviz -L/home/toedling/local/lib -o RCurl.so base64.o curl_base64.o curl.o curlInit.o enums.o memoryManagement.o -L/usr/lib64 -lcurl -lidn -lssl -lcrypto -ldl -lz > ** R > ** inst > ** preparing package for lazy loading > ** help > >>> Building/Updating help pages for package 'RCurl' > Formats: text html latex example > Note: removing empty section \examples > Note: removing empty section \references > Note: removing empty section \seealso > Note: removing empty section \examples > Note: unmatched right brace in 'MultiCURLHandle-class' on or after line 28 > Note: removing empty section \examples > Note: removing empty section \examples > Note: removing empty section \examples > Note: removing empty section \examples > ** building package indices ... > * DONE (RCurl) > > > > Martin Morgan wrote: >> Hi Mark... >> >> A couple of shots in the dark, as no one else seems to be leaping in... >> >> The symbol Curl_base64_encode should be defined in >> /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so. What >> does >> >> nm /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so >> >> say? Mine says >> >> 0000000000003980 T Curl_base64_encode >> >> with the 'T' indicating that the symbol is defined (make sure nm spits >> out a bunch of lines before concluding that Curl_base64_encode is not >> defined). >> >> I retrieved the RCurl source, and one thing I notice is that >> RCurl/src/curl_base64.c has the 'execute' bit set, and perhaps a sane >> system would not compile it. Try >> >> % chmod -x RCurl/src/curl_base64.c >> >> and then >> >> % R CMD INSTALL RCurl >> >> Martin >> >> "Mark Kimpel" <mwkimpel at="" gmail.com=""> writes: >> >> >>> I'm having same problem on Ubuntu 64-bit Hardy Heron. A bunch of security >>> patches from Ubuntu came out and I installed them today. After that was when >>> I first noted the problem (affycoretools, which I use all the time, won't >>> load). Below is my initial output, what follows is my reinstallation output >>> followed by the same error messages as obtained intially. I wonder if a >>> security patch has changed Curl? Or did RCurl just change? I have been using >>> R-2.7.0 since half-way through its develoment cycle and this is a new >>> problem for me. >>> >>> Mark >>> >>> >>>> require(RCurl) >>>> >>> Loading required package: RCurl >>> Error in dyn.load(file, DLLpath = DLLpath, ...) : >>> unable to load shared library >>> '/home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so': >>> /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so: undefined >>> symbol: Curl_base64_encode >>> >>>> install.packages("RCurl") >>>> > > _______________________________________________ > 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 -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M2 B169 Phone: (206) 667-2793