From duncan at wald.ucdavis.edu  Wed May  7 08:27:05 2008
From: duncan at wald.ucdavis.edu (Duncan Temple Lang)
Date: Wed, 07 May 2008 18:27:05 +1200
Subject: [Rd] [R] [BioC] RCurl loading problem with 64 bit linux
	distribution
In-Reply-To: <alpine.LFD.1.10.0805070655060.12257@gannet.stats.ox.ac.uk>
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>
	<alpine.LFD.1.10.0805070655060.12257@gannet.stats.ox.ac.uk>
Message-ID: <48214BB9.8040507@wald.ucdavis.edu>

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Prof Brian Ripley wrote:
| Let's move this to R-devel.  It's programming (not even R programming),
| and getting complex.
|

Indeed!

| 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

Not quite. It uses curl-config. We could move to a two tier system
of using pkg-config and then curl-config, but that hasn't been necessary yet.

| 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.)
|

All previous versions are also available from the www.omegahat.org/R
source repository.

~ D.

|
| 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:
|>
|
| 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
| |>
| |
| |
| |
|>>
|>
|>
|>
|> --
|> 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.
|>

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[Rd] [R] [BioC] RCurl loading problem with 64 bit linux distribution
Duncan Temple Lang