RCurl loading problem with 64 bit linux distribution
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John Lande ▴ 280
@john-lande-2357
Last seen 10.2 years ago
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]]
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Loyal Goff ▴ 10
@loyal-goff-2784
Last seen 10.2 years ago
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
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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_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 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@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/R Curl.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/RC url.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=e n_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_ID ENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@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@rci.rutgers.edu > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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]]
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@martin-morgan-1513
Last seen 4 months ago
United States
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
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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_COL LATE=en_US.ISO-8859-1;LC_MONETARY=C;LC_MESSAGES=en_US.ISO-8859-1;LC_PA PER=en_US.ISO-8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREM ENT=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") >>>
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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
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 I just put a new version of the RCurl package that is intended to by-pass the issues with differences in libcurls and takes the base64 encoding source into the package itself. As I cannot reproduce the problem readily on amy of my current machine configurations and the package works for me on RedHat and OSX, I'd appreciate hearing if the new version solves the problems. It is available as ~ install.packages("RCurl", repos = "http://www.omegahat.org/R") ~ D. Martin Morgan wrote: | 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_COL LATE=en_US.ISO-8859-1;LC_MONETARY=C;LC_MESSAGES=en_US.ISO-8859-1;LC_PA PER=en_US.ISO-8859-1;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREM ENT=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 | -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.7 (Darwin) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFIIb7+9p/Jzwa2QP4RAuIpAJ0QpWZEb/cxQ+VOkx+JkiJLKKDThACfdKdq byokNcbYyZ4ebhN3fanJA1A= =LBuS -----END PGP SIGNATURE-----
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Entering edit mode
On May 7, 2008, at 7:38 AM, Duncan Temple Lang wrote: > -----BEGIN PGP SIGNED MESSAGE----- > Hash: SHA1 > > > I just put a new version of the RCurl package that is intended to > by-pass the issues with differences in libcurls and takes the > base64 encoding source into the package itself. As I cannot > reproduce the problem readily on amy of my current machine > configurations > and the package works for me on RedHat and OSX, I'd appreciate > hearing if the new version solves the problems. > It is available as > > ~ install.packages("RCurl", repos = "http://www.omegahat.org/R") Hi Duncan I can reproduce the problem. I have just compiled R-2.7.0-patch as well as R-2.8.0 from svn (both obtained yesterday). RCurl version 0.8-3 works fine on 2.7 but not on 2.8. The new RCurl version 0.9-2 works fine with both version. Kasper > ~ D. > > Martin Morgan wrote: > | 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_COLLATE > = > 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_MEASUREMENT=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 > | > -----BEGIN PGP SIGNATURE----- > Version: GnuPG v1.4.7 (Darwin) > Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org > > iD8DBQFIIb7+9p/Jzwa2QP4RAuIpAJ0QpWZEb/cxQ+VOkx+JkiJLKKDThACfdKdq > byokNcbYyZ4ebhN3fanJA1A= > =LBuS > -----END PGP SIGNATURE----- > > _______________________________________________ > 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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