[BioC] RCurl loading problem with 64 bit linux distribution
Let's move this to R-devel. It's programming (not even R programming), and getting complex. One crucial issue issue is how you installed R -- from sources or as a binary. Also, I am assuming that this is x86_64 (there are other '64-bit' Linuxen). Library paths are determined by LD_LIBRARY_PATH, amongst other things (and not by PATH on Linux). With R built from the sources, this will include /usr/local/lib64, but I believe that for a binary build it does not -- look in R_HOME/etc/ldpaths to see. Also, you seem to have compiled curl to be in /usr/local/lib -- if this is an x86_64 system that might well not be found -- it is not where R's paths look. (It's a common issue with compiling autoconf-ed packages -- you need to set --libdir=/usr/local/lib64, say.) RCurl uses pkg_config to to find libcurl, and that does not by default look in /usr/local. So it is likely that it looked at the Ubuntu version and not the one you installed. I don't think that curl 7.18.1 is enough of an improvement to make all these hassles worthwhile -- I would do a 'make uninstall' on your own version. DTL and I have been having some private correspondence about this. At present RCurl_0.9-1 still segfaults for me because the configure detection isn't detecting (this is F8, curl 7.17.1). 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, it not obvious on the web pages.)
On Wed, 7 May 2008, Mark Kimpel wrote:
Duncan, I know have two version of libcurl on my system, the Ubuntu installed 7.18.0 and my newly compiled from source 7.18.1 (which I installed after my problems began with RCurl). I was afraid to uninstall 7.18.0 because Synaptic wanted to uninstall half of my system if I did so via my package manger. I must not have my PATH set up correctly because when I do curl --version, I get: curl 7.18.1 (x86_64-unknown-linux-gnu) libcurl/7.18.0 OpenSSL/0.9.8g zlib/ 1.2.3.3 libidn/1.1 Protocols: tftp ftp telnet dict ldap ldaps http file https ftps Features: GSS-Negotiate IDN IPv6 Largefile NTLM SSL libz So curl is new and libcurl is a version older. This probably isn't ideal, but may help us figure out what is going on because I ran nm against both versions of libcurl.... for libcurl 7.18.1: mkimpel-m90 /usr/local/lib: nm libcurl.so | grep Curl_base64_encode 0000000000009e30 T Curl_base64_encode for libcurl 7.18.0 mkimpel-m90 /usr/lib: nm libcurl.so | grep Curl_base64_encode nm: libcurl.so: no symbols
That doesn't help, because Linux distros strip symbols.
it looks like RCurl is still trying to link against 7.18.0, but, do I interpret your comments to mean that, if I set up my PATH correctly so that the newer version is found first, things might work? Regardless, I hope this is somewhat diagnostic. If I have screwed up the setup too much to make sense out of, perhaps one of the other guys with problems could also furnish the info. BTW, I did cc you on my post to R-help this evening (see below). Thanks for your help and all your development efforts, Mark romMark Kimpel <mwkimpel at gmail.com>toLoyal Goff <lgoff at rci.rutgers.edu>, ccbioconductor at stat.math.ethz.ch, duncan at wald.ucdavis.edu, dateTue, May 6, 2008 at 9:18 PM On Wed, May 7, 2008 at 12:43 AM, Duncan Temple Lang <duncan at wald.ucdavis.edu> wrote:
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1
Hi all
~ I'm glad this made it to R-help (or R-devel) so that I saw it
as this is the sort of problem that should be at least CC'ed to the
package maintainer.
~ Yes, there was a change to RCurl yesterday with one of the changes
being to synchronize code between libcurl and RCurl regarding base64
encoding
which was causing a segfault with recent versions of libcurl.
~ The latest RCurl does not include the code for the Curl_base64_encode
which was in the curl_base64.c file. The intent was to link against
the on in libcurl, but what your reports suggest is that one some
systems this is not available from libcurl.so. Can you confirm this with
the nm output from libcurl.so
~ nm libcurl.so | grep Curl_base64_encode
Precisely where libcurl.so (or libcurl.so.<digit>...) will vary,
but it is probably in /usr/local/lib/ and you can see
by using
~ curl-config --libs
and seeing if there is -L<directory/path> in the output which will
tell you where it is likely to be.
If the symbol (Curl_base64_encode) is not there, there will be no output!
~ If that is the case, we will have to back to having our own copy
of that routine and so we will end up with two versions - one for
the old and one for the new and the configuration will endeavor to
determine which is appropriate.
~ HTH
~ D.
Mark Kimpel wrote:
| 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 <mtmorgan at fhcrc.org>
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")
|>>> 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 <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
|>>> 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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-- 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]]
______________________________________________ R-help at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595