From ripley at stats.ox.ac.uk  Wed May  7 08:18:29 2008
From: ripley at stats.ox.ac.uk (Prof Brian Ripley)
Date: Wed, 7 May 2008 07:18:29 +0100 (BST)
Subject: [Rd] [R] [BioC] RCurl loading problem with 64 bit linux
 distribution
In-Reply-To: <6b93d1830805062227g46860d14s2f7d9085c263e26b@mail.gmail.com>
References: <c2ebc3880805060248w2bb45baan42f9e4c64b57f2d0@mail.gmail.com>
	<1F13A373-3556-4132-BAE1-76B4BB5C87E3@rci.rutgers.edu>
	<6b93d1830805061818k26b1ead4xa1a2cf55234e3e47@mail.gmail.com>
	<6phlk2mu9gq.fsf@gopher4.fhcrc.org>
	<6b93d1830805062059g2cc2fafevae498cfae041c1de@mail.gmail.com>
	<4821338D.4090400@wald.ucdavis.edu>
	<6b93d1830805062227g46860d14s2f7d9085c263e26b@mail.gmail.com>
Message-ID: <alpine.LFD.1.10.0805070655060.12257@gannet.stats.ox.ac.uk>

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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>>
>> iD8DBQFIITON9p/Jzwa2QP4RApOIAJ9d7OQ/3Q7bbIV4I6WreygKUgMG7QCdHJxL
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>> =Anh4
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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



[Rd] [R] [BioC] RCurl loading problem with 64 bit linux distribution
Prof Brian Ripley