[R] installing RCurl when libcurl is in non-standard location
Janet Young
jayoung at fhcrc.org
Thu Jan 14 03:24:14 CET 2010
Hi,
I'm struggling to install RCurl for 32-bit linux and am hoping for
some suggestions.
I obtained RCurl_1.3-1.tar.gz from CRAN today, and am using a very
recent version of R:
R version 2.10.1 Patched (2010-01-12 r50970).
I'm not the sysadmin for this system (disclaimer: my sysadmin skills
are not very good, I'm afraid). curl is available centrally on the
system but it's a little old (7.12.3 - looks from some older r-help
posts like this is too old for RCurl). Therefore I installed libcurl
7.19.7 in a non-standard location (because I'm not the sysadmin), and
I think I'm pointing R towards this new libcurl OK, but I'm not 100%
sure about that. The output of locate (see below) makes me a little
suspicious, but the output of the R CMD INSTALL makes it seem like the
new libcurl I installed IS being used.
I've included various output below that I hope will help in figuring
this out. Is there anything else that would be useful to know? I can
also ask our sysadmin for help if that makes more sense than asking
you all via r-help.
Thanks very much in advance for any ideas,
Janet Young
---------------
[2] zork20:/home/jayoung> uname -a
Linux zork20 2.6.12-1.1381_FC3smp #1 SMP Fri Oct 21 04:03:26 EDT 2005
i686 athlon i386 GNU/Linux
[3] zork20:/home/jayoung> setenv MAKE gmake
[4] zork20:/home/jayoung> which gmake
/usr/bin/gmake
[5] zork20:/home/jayoung> gmake -version
GNU Make 3.80
Copyright (C) 2002 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.
There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.
[6] zork20:/home/jayoung> which curl-config
/home/jayoung/traskdata/bin_linux/curl-config
[7] zork20:/home/jayoung> curl-config --version
libcurl 7.19.7
[8] zork20:/home/jayoung> locate curl-config
/usr/bin/curl-config
/usr/share/man/man1/curl-config.1.gz
[16] zork20:/home/jayoung> /usr/bin/curl-config --version
libcurl 7.12.3
[9] zork20:/home/jayoung> locate libcurl
/usr/lib/libcurl.so.3
/usr/lib/libcurl.so
/usr/lib/libcurl.a
/usr/lib/libcurl.so.3.0.0
/usr/share/man/man3/libcurl-multi.3.gz
/usr/share/man/man3/libcurl-easy.3.gz
/usr/share/man/man3/libcurl-errors.3.gz
/usr/share/man/man3/libcurl-share.3.gz
/usr/share/man/man3/libcurl-tutorial.3.gz
/usr/share/man/man3/libcurl.3.gz
[10] zork20:/home/jayoung> ls ~/traskdata/lib_linux/libcu*
/home/jayoung/traskdata/lib_linux/libcurl.a
/home/jayoung/traskdata/lib_linux/libcurl.la*
/home/jayoung/traskdata/lib_linux/libcurl.so@
/home/jayoung/traskdata/lib_linux/libcurl.so.3@
/home/jayoung/traskdata/lib_linux/libcurl.so.3.0.0*
/home/jayoung/traskdata/lib_linux/libcurl.so.4@
/home/jayoung/traskdata/lib_linux/libcurl.so.4.0.0*
/home/jayoung/traskdata/lib_linux/libcurl.so.4.1.1*
[11] zork20:/home/jayoung> printenv LD_LIBRARY_PATH
/home/btrask/traskdata/lib_linux:/home/jayoung/traskdata/bin_linux/qt/
lib:/home/btrask/traskdata/lib_linux/R/library/RSPerl/libs:/home/
btrask/traskdata/lib_linux/R/lib
[14] zork20:/home/jayoung/source_codes/R/other_packages> R CMD INSTALL
RCurl_1.3-1.tar.gz --configure-args='--libdir=/home/btrask/traskdata/
lib_linux --includedir=/home/btrask/traskdata/include'
* installing to library ‘/home/btrask/traskdata/lib_linux/R/library’
* installing *source* package ‘RCurl’ ...
checking for curl-config... /home/jayoung/traskdata/bin_linux/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
Version has CURLOPT_URL
Version has CURLINFO_EFFECTIVE_URL
Version has CURLINFO_RESPONSE_CODE
Version has CURLINFO_TOTAL_TIME
Version has CURLINFO_NAMELOOKUP_TIME
Version has CURLINFO_CONNECT_TIME
Version has CURLINFO_PRETRANSFER_TIME
Version has CURLINFO_SIZE_UPLOAD
Version has CURLINFO_SIZE_DOWNLOAD
Version has CURLINFO_SPEED_DOWNLOAD
Version has CURLINFO_SPEED_UPLOAD
Version has CURLINFO_HEADER_SIZE
Version has CURLINFO_REQUEST_SIZE
Version has CURLINFO_SSL_VERIFYRESULT
Version has CURLINFO_FILETIME
Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD
Version has CURLINFO_CONTENT_LENGTH_UPLOAD
Version has CURLINFO_STARTTRANSFER_TIME
Version has CURLINFO_CONTENT_TYPE
Version has CURLINFO_REDIRECT_TIME
Version has CURLINFO_REDIRECT_COUNT
Version has CURLINFO_PRIVATE
Version has CURLINFO_HTTP_CONNECTCODE
Version has CURLINFO_HTTPAUTH_AVAIL
Version has CURLINFO_PROXYAUTH_AVAIL
Version has CURLINFO_OS_ERRNO
Version has CURLINFO_NUM_CONNECTS
Version has CURLINFO_SSL_ENGINES
No CURLINFO_COOKIELIST enumeration value.
No CURLINFO_LASTSOCKET enumeration value.
No CURLINFO_FTP_ENTRY_PATH enumeration value.
No CURLINFO_REDIRECT_URL enumeration value.
No CURLINFO_PRIMARY_IP enumeration value.
No CURLINFO_APPCONNECT_TIME enumeration value.
No CURLINFO_CERTINFO enumeration value.
No CURLINFO_CONDITION_UNMET enumeration value.
No CURLOPT_KEYPASSWD enumeration value.
No CURLOPT_DIRLISTONLY enumeration value.
No CURLOPT_APPEND enumeration value.
No CURLOPT_KRBLEVEL enumeration value.
No CURLOPT_USE_SSL enumeration value.
No CURLOPT_TIMEOUT_MS enumeration value.
No CURLOPT_CONNECTTIMEOUT_MS enumeration value.
No CURLOPT_HTTP_TRANSFER_DECODING enumeration value.
No CURLOPT_HTTP_CONTENT_DECODING enumeration value.
No CURLOPT_NEW_FILE_PERMS enumeration value.
No CURLOPT_NEW_DIRECTORY_PERMS enumeration value.
No CURLOPT_POSTREDIR enumeration value.
No CURLOPT_OPENSOCKETFUNCTION enumeration value.
No CURLOPT_OPENSOCKETDATA enumeration value.
No CURLOPT_COPYPOSTFIELDS enumeration value.
No CURLOPT_PROXY_TRANSFER_MODE enumeration value.
No CURLOPT_SEEKFUNCTION enumeration value.
No CURLOPT_SEEKDATA enumeration value.
No CURLOPT_CRLFILE enumeration value.
No CURLOPT_ISSUERCERT enumeration value.
No CURLOPT_ADDRESS_SCOPE enumeration value.
No CURLOPT_CERTINFO enumeration value.
No CURLOPT_USERNAME enumeration value.
No CURLOPT_PASSWORD enumeration value.
No CURLOPT_PROXYUSERNAME enumeration value.
No CURLOPT_PROXYPASSWORD enumeration value.
No CURLOPT_SSH_HOST_PUBLIC_KEY_MD5 enumeration value.
No CURLOPT_NOPROXY enumeration value.
No CURLOPT_TFTP_BLKSIZE enumeration value.
No CURLOPT_SOCKS5_GSSAPI_SERVICE enumeration value.
No CURLOPT_SOCKS5_GSSAPI_NEC enumeration value.
No CURLOPT_PROTOCOLS enumeration value.
No CURLOPT_REDIR_PROTOCOLS enumeration value.
No CURLOPT_SSH_AUTH_TYPES enumeration value.
No CURLOPT_SSH_PUBLIC_KEYFILE enumeration value.
No CURLOPT_SSH_PRIVATE_KEYFILE enumeration value.
No CURLOPT_FTP_SSL_CCC enumeration value.
No CURLOPT_COOKIELIST enumeration value.
No CURLOPT_IGNORE_CONTENT_LENGTH enumeration value.
No CURLOPT_FTP_SKIP_PASV_IP enumeration value.
No CURLOPT_FTP_FILEMETHOD enumeration value.
No CURLOPT_LOCALPORT enumeration value.
No CURLOPT_LOCALPORTRANGE enumeration value.
No CURLOPT_CONNECT_ONLY enumeration value.
No CURLOPT_CONV_FROM_NETWORK_FUNCTION enumeration value.
No CURLOPT_CONV_TO_NETWORK_FUNCTION enumeration value.
No CURLOPT_CONV_FROM_UTF8_FUNCTION enumeration value.
No CURLOPT_MAX_SEND_SPEED_LARGE enumeration value.
No CURLOPT_MAX_RECV_SPEED_LARGE enumeration value.
No CURLOPT_FTP_ALTERNATIVE_TO_USER enumeration value.
No CURLOPT_SOCKOPTFUNCTION enumeration value.
No CURLOPT_SOCKOPTDATA enumeration value.
No CURLOPT_SSL_SESSIONID_CACHE enumeration value.
libcurl version: libcurl 7.19.7
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/home/btrask/traskdata/lib_linux/R/include -I/usr/
local/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -
DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -
DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -
DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -
DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -
DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -
DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -
DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -
DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -
DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -
DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -
DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -
DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -
DHAVE_CURLINFO_SSL_ENGINES=1 -I/usr/local/include -fpic -g -O2 -c
base64.c -o base64.o
gcc -std=gnu99 -I/home/btrask/traskdata/lib_linux/R/include -I/usr/
local/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -
DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -
DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -
DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -
DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -
DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -
DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -
DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -
DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -
DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -
DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -
DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -
DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -
DHAVE_CURLINFO_SSL_ENGINES=1 -I/usr/local/include -fpic -g -O2 -c
curl.c -o curl.o
curl.c:585: warning: "struct curl_certinfo" declared inside parameter
list
curl.c:585: warning: its scope is only this definition or declaration,
which is probably not what you want
gcc -std=gnu99 -I/home/btrask/traskdata/lib_linux/R/include -I/usr/
local/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -
DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -
DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -
DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -
DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -
DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -
DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -
DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -
DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -
DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -
DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -
DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -
DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -
DHAVE_CURLINFO_SSL_ENGINES=1 -I/usr/local/include -fpic -g -O2 -c
curlInit.c -o curlInit.o
gcc -std=gnu99 -I/home/btrask/traskdata/lib_linux/R/include -I/usr/
local/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -
DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -
DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -
DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -
DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -
DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -
DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -
DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -
DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -
DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -
DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -
DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -
DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -
DHAVE_CURLINFO_SSL_ENGINES=1 -I/usr/local/include -fpic -g -O2 -c
curl_base64.c -o curl_base64.o
gcc -std=gnu99 -I/home/btrask/traskdata/lib_linux/R/include -I/usr/
local/include -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -
DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -
DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -
DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -
DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -
DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -
DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -
DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -
DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -
DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -
DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -
DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -
DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -
DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -
DHAVE_CURLINFO_SSL_ENGINES=1 -I/usr/local/include -fpic -g -O2 -c
enums.c -o enums.o
In file included from CurlOptEnums.h:10,
from enums.c:79:
CURLOptTable.h:131: error: `CURLOPT_FTP_ACCOUNT' undeclared here (not
in a function)
CURLOptTable.h:131: error: initializer element is not constant
CURLOptTable.h:131: error: (near initialization for
`CurlOptionNames[110].val')
CURLOptTable.h:131: error: initializer element is not constant
CURLOptTable.h:131: error: (near initialization for
`CurlOptionNames[110]')
CURLOptTable.h:325: error: initializer element is not constant
CURLOptTable.h:325: error: (near initialization for
`CurlOptionNames[111]')
CURLOptTable.h:341: error: initializer element is not constant
CURLOptTable.h:341: error: (near initialization for
`CurlOptionNames[112]')
CURLOptTable.h:357: error: initializer element is not constant
CURLOptTable.h:357: error: (near initialization for
`CurlOptionNames[113]')
gmake: *** [enums.o] Error 1
ERROR: compilation failed for package ‘RCurl’
* removing ‘/home/btrask/traskdata/lib_linux/R/library/RCurl’
* restoring previous ‘/home/btrask/traskdata/lib_linux/R/library/RCurl’
(I get similar errors if I omit the --configure-args from the R CMD
INSTALL command)
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