[BioC] RCurl loading problem with 64 bit linux distribution
Martin Morgan
mtmorgan at fhcrc.org
Wed May 7 04:36:05 CEST 2008
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_IDENTIFICATION=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
>
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>
> Natural language support but running in an English locale
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>
> 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/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
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
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>> 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
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--
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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