Martin,
Well, thanks for jumping in! We need all the help we can get ;)
I changed the execute bit as you suggested and recompiled, no luck, still
the same error message.
Below is the output you wanted me to look at, its a bit beyond me so I
include both a brief grep summary and then the whole enchilada. I do note
that my output is different from yours, but I'm not sure how to interpret.
I also thought about removing curl from my system, but when starting to do
so with Synaptic, it looked like if I removed libcurl I would trash an awful
lot of my system. I did download and install the latest curl 7.18.1 on top
of the other one, put /usr/local/ to the start of my PATH, reinstalled
RCurl, and still the same erro message comes up.
So, what does it mean that the output of nm is different on our systems and
is it important?
Thanks, Mark
mkimpel-m90 ~/bin/curl-7.18.1: nm
/home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so | grep
base64_encode
U Curl_base64_encode
0000000000003910 T R_base64_encode
mkimpel-m90 ~/bin/curl-7.18.1: nm
/home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so | grep
Curl_base64_encode
U Curl_base64_encode
mkimpel-m90 ~/bin/curl-7.18.1: nm
/home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so
U CDR
0000000000208aa0 d CallEntries
0000000000208c00 D CurlErrorNames
000000000020aac0 D CurlInfoNames
0000000000209740 D CurlOptionNames
U Curl_base64_decode
U Curl_base64_encode
U INTEGER
U LENGTH
U LOGICAL
000000000020aee8 B OptionMemoryManager
U PRINTNAME
U RAW
0000000000003f70 T RCreateNamesVec
00000000002086a0 d RCurlErrorBuffer
0000000000003fe0 T RCurlVersionInfoToR
0000000000006d00 T RCurl_addMemoryAllocation
0000000000006c90 T RCurl_addMemoryTicket
0000000000006b50 T RCurl_getMemoryManager
0000000000006b80 T RCurl_releaseManagerMemoryTickets
0000000000006c70 T RCurl_releaseMemoryTickets
U REAL
U R_CHAR
U R_ClassSymbol
U R_ExternalPtrAddr
U R_ExternalPtrTag
U R_GlobalEnv
U R_MakeExternalPtr
U R_NaInt
U R_NamesSymbol
U R_NilValue
U R_PreserveObject
U R_RegisterCFinalizer
U R_ReleaseObject
U R_alloc
0000000000003a90 T R_base64_decode
0000000000003910 T R_base64_encode
0000000000005060 T R_call_R_write_function
0000000000003bc0 T R_check_bits
00000000000047f0 T R_curlMultiPerform
0000000000004db0 T R_curl_BinaryData_free
0000000000004c90 T R_curl_BinaryData_new
0000000000005380 T R_curl_BinaryData_to_raw
0000000000004dd0 T R_curl_debug_callback
0000000000006970 T R_curl_easy_duphandle
0000000000005680 T R_curl_easy_getinfo
00000000000069a0 T R_curl_easy_init
0000000000006880 T R_curl_easy_perform
00000000000060e0 T R_curl_easy_setopt
0000000000005710 T R_curl_escape
0000000000005440 T R_curl_getpasswd
0000000000006950 T R_curl_global_cleanup
0000000000006930 T R_curl_global_init
0000000000004af0 T R_curl_progress_callback
00000000000042f0 T R_curl_ssl_ctx_callback
0000000000005c10 T R_curl_version
0000000000005bf0 T R_curl_version_info
0000000000005270 T R_curl_write_binary_data
00000000000051b0 T R_curl_write_data
00000000000051d0 T R_curl_write_header_data
U R_do_MAKE_CLASS
U R_do_new_object
U R_do_slot
U R_do_slot_assign
0000000000004530 t R_finalizeCurlHandle
0000000000006af0 T R_getCURLErrorEnum
0000000000006b10 T R_getCURLInfoEnum
0000000000006b30 T R_getCURLOptionEnum
0000000000003ea0 T R_getCurlMultiHandle
0000000000006a00 T R_init_RCurl
0000000000003bf0 T R_internalWriteTest
0000000000004a50 T R_popCurlMultiHandle
0000000000006600 T R_post_form
0000000000004aa0 T R_pushCurlMultiHandle
U R_registerRoutines
U R_tryEval
U R_useDynamicSymbols
00000000000057e0 T Rcurl_set_header
U Rf_ScalarInteger
U Rf_ScalarReal
U Rf_ScalarString
U Rf_allocVector
U Rf_asInteger
U Rf_error
U Rf_eval
U Rf_getAttrib
U Rf_install
U Rf_length
U Rf_mkChar
U Rf_mkCharCE
U Rf_mkCharLen
U Rf_mkString
U Rf_protect
U Rf_setAttrib
U Rf_unprotect
U Rf_warning
U SETCAR
U SET_STRING_ELT
U SET_VECTOR_ELT
U STRING_ELT
U TYPEOF
U VECTOR_ELT
0000000000208040 d VersionInfoFieldNames
00000000002080c0 a _DYNAMIC
0000000000208308 a _GLOBAL_OFFSET_TABLE_
w _Jv_RegisterClasses
0000000000208008 d __CTOR_END__
0000000000208000 d __CTOR_LIST__
0000000000208018 d __DTOR_END__
0000000000208010 d __DTOR_LIST__
0000000000007e58 r __FRAME_END__
0000000000208020 d __JCR_END__
0000000000208020 d __JCR_LIST__
000000000020aee0 A __bss_start
w __cxa_finalize@@GLIBC_2.2.5
0000000000006e20 t __do_global_ctors_aux
0000000000003890 t __do_global_dtors_aux
0000000000208680 d __dso_handle
w __gmon_start__
U __stack_chk_fail@@GLIBC_2.4
U __strdup@@GLIBC_2.2.5
000000000020aee0 A _edata
000000000020aef0 A _end
0000000000006e58 T _fini
0000000000003188 T _init
0000000000005c30 T addFormElement
0000000000006050 T buildForm
0000000000003870 t call_gmon_start
U calloc@@GLIBC_2.2.5
0000000000004f90 T checkEncoding
000000000020aee0 b completed.6183
0000000000006a30 T createNamedEnum
U curl_easy_cleanup@@CURL_GNUTLS_3
U curl_easy_duphandle@@CURL_GNUTLS_3
U curl_easy_getinfo@@CURL_GNUTLS_3
U curl_easy_init@@CURL_GNUTLS_3
U curl_easy_perform@@CURL_GNUTLS_3
U curl_easy_setopt@@CURL_GNUTLS_3
U curl_easy_strerror@@CURL_GNUTLS_3
U curl_escape@@CURL_GNUTLS_3
U curl_formadd@@CURL_GNUTLS_3
U curl_formfree@@CURL_GNUTLS_3
U curl_free@@CURL_GNUTLS_3
U curl_global_cleanup@@CURL_GNUTLS_3
U curl_global_init@@CURL_GNUTLS_3
U curl_multi_add_handle@@CURL_GNUTLS_3
U curl_multi_fdset@@CURL_GNUTLS_3
U curl_multi_init@@CURL_GNUTLS_3
U curl_multi_perform@@CURL_GNUTLS_3
U curl_multi_remove_handle@@CURL_GNUTLS_3
U curl_slist_append@@CURL_GNUTLS_3
U curl_slist_free_all@@CURL_GNUTLS_3
U curl_unescape@@CURL_GNUTLS_3
U curl_version@@CURL_GNUTLS_3
U curl_version_info@@CURL_GNUTLS_3
U fprintf@@GLIBC_2.2.5
00000000000038e0 t frame_dummy
U free@@GLIBC_2.2.5
0000000000004590 T getBinaryDataFromR
00000000000043f0 T getCURLPointerRObject
00000000000053e0 T getCurlError
0000000000005560 T getCurlInfoElement
0000000000005900 T getCurlPointerForData
0000000000003c40 T getMultiCURLPointerRObject
0000000000003ec0 T getRStringsFromNullArray
0000000000004190 T makeCURLPointerRObject
00000000000047b0 T makeCURLcodeRObject
0000000000003d80 T makeMultiCURLPointerRObject
U malloc@@GLIBC_2.2.5
U memcpy@@GLIBC_2.2.5
00000000002080a0 d names.7400
0000000000208688 d p.6181
U realloc@@GLIBC_2.2.5
U select@@GLIBC_2.2.5
U sprintf@@GLIBC_2.2.5
U stderr@@GLIBC_2.2.5
U strcpy@@GLIBC_2.2.5
U strlen@@GLIBC_2.2.5
U strncpy@@GLIBC_2.2.5
mkimpel-m90 ~/bin/curl-7.18.1:
On Tue, May 6, 2008 at 10:36 PM, Martin Morgan <[EMAIL PROTECTED]> 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" <[EMAIL PROTECTED]> 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
> >
> > 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 <[EMAIL PROTECTED]>
> 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
> >> > [EMAIL PROTECTED]
> >> > 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
> >> [EMAIL PROTECTED]
> >>
> >>
> >> _______________________________________________
> >> Bioconductor mailing list
> >> [EMAIL PROTECTED]
> >> 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
> > [EMAIL PROTECTED]
> > 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
>
--
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)
******************************************************************
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