[Bioc-devel] Need help on biomaRt
Hi Sean,
Thanks for the pointer!
I have installed Rcompression. However R CMD check RCurl R CMD install still failed. Anyone tried to install the RCurl version 0.97-3 in Mac OS 10.4 with a success? Attached is the detailed error message during check. Thanks a lot for your help!
Best regards,
Julie
new-host-3:~/Documents/download _lzh217$ R CMD check RCurl
* checking for working pdflatex ... OK
* using log directory '/Users/_lzh217/Documents/download/RCurl.Rcheck'
* using R version 2.10.0 Under development (unstable) (2009-05-20 r48588)
* using session charset: ASCII
* checking for file 'RCurl/DESCRIPTION' ... OK
* this is package 'RCurl' version '0.97-3'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... WARNING
Subdirectory 'RCurl/src' contains object files.
* checking for executable files ... OK
* checking whether package 'RCurl' can be installed ...... ERROR
Installation failed.
See '/Users/_lzh217/Documents/download/RCurl.Rcheck/00install.out' for details.
new-host-3:~/Documents/download _lzh217$ R CMD install -l /Library/Frameworks/R.framework/Versions/Current/Resources/library/ RCurl
* 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
Version has CURLOPT_URL
No CURLOPT_NOPROXY enumeration value.
No CURLINFO_CONDITION_UNMET enumeration value.
No CURLINFO_REDIRECT_URL enumeration value.
No CURLINFO_CERTINFO enumeration value.
No CURLINFO_PRIMARY_IP enumeration value.
No CURLINFO_APPCONNECT_TIME 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_SSH_HOST_PUBLIC_KEY_MD 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.
configure: creating ./config.status
config.status: creating src/Makevars
** libs
** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=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:132: error: 'CURLOPT_COOKIELIST' undeclared here (not in a function)
CURLOptTable.h:133: error: 'CURLOPT_IGNORE_CONTENT_LENGTH' undeclared here (not in a function)
CURLOptTable.h:134: error: 'CURLOPT_FTP_SKIP_PASV_IP' undeclared here (not in a function)
CURLOptTable.h:135: error: 'CURLOPT_FTP_FILEMETHOD' undeclared here (not in a function)
CURLOptTable.h:136: error: 'CURLOPT_LOCALPORT' undeclared here (not in a function)
CURLOptTable.h:137: error: 'CURLOPT_LOCALPORTRANGE' undeclared here (not in a function)
CURLOptTable.h:138: error: 'CURLOPT_CONNECT_ONLY' undeclared here (not in a function)
CURLOptTable.h:139: error: 'CURLOPT_CONV_FROM_NETWORK_FUNCTION' undeclared here (not in a function)
CURLOptTable.h:140: error: 'CURLOPT_CONV_TO_NETWORK_FUNCTION' undeclared here (not in a function)
CURLOptTable.h:141: error: 'CURLOPT_CONV_FROM_UTF8_FUNCTION' undeclared here (not in a function)
CURLOptTable.h:142: error: 'CURLOPT_MAX_SEND_SPEED_LARGE' undeclared here (not in a function)
CURLOptTable.h:143: error: 'CURLOPT_MAX_RECV_SPEED_LARGE' undeclared here (not in a function)
CURLOptTable.h:144: error: 'CURLOPT_FTP_ALTERNATIVE_TO_USER' undeclared here (not in a function)
CURLOptTable.h:145: error: 'CURLOPT_SOCKOPTFUNCTION' undeclared here (not in a function)
CURLOptTable.h:146: error: 'CURLOPT_SOCKOPTDATA' undeclared here (not in a function)
CURLOptTable.h:147: error: 'CURLOPT_SSL_SESSIONID_CACHE' undeclared here (not in a function)
CURLOptTable.h:148: error: 'CURLOPT_SSH_AUTH_TYPES' undeclared here (not in a function)
CURLOptTable.h:149: error: 'CURLOPT_SSH_PUBLIC_KEYFILE' undeclared here (not in a function)
CURLOptTable.h:150: error: 'CURLOPT_SSH_PRIVATE_KEYFILE' undeclared here (not in a function)
CURLOptTable.h:151: error: 'CURLOPT_FTP_SSL_CCC' undeclared here (not in a function)
In file included from CurlInfoEnums.h:33,
from enums.c:80:
CURLINFOTable.h:28: error: 'CURLINFO_COOKIELIST' undeclared here (not in a function)
CURLINFOTable.h:29: error: 'CURLINFO_LASTSOCKET' undeclared here (not in a function)
CURLINFOTable.h:30: error: 'CURLINFO_FTP_ENTRY_PATH' undeclared here (not in a function)
make: *** [enums.o] Error 1
ERROR: compilation failed for package 'RCurl'
* removing '/Library/Frameworks/R.framework/Versions/2.10/Resources/library/RCurl'
* restoring previous '/Library/Frameworks/R.framework/Versions/2.10/Resources/library/RCurl'
-----Original Message-----
From: Sean Davis [mailto:seandavi at gmail.com]
Sent: Tue 6/2/2009 11:16 AM
To: Zhu, Julie
Cc: Florian Hahne; bioc-devel at stat.math.ethz.ch
Subject: Re: [Bioc-devel] Need help on biomaRt
On Tue, Jun 2, 2009 at 11:06 AM, Zhu, Julie <Julie.Zhu at umassmed.edu> wrote:
Hi Florian, The following error occurred when I tried to perform R CMD check RCurl for the version 0.97-3. Do you have any suggestion to get Rcompression? Thanks! new-host-3:~/Documents/download _lzh217$ ?R CMD check RCurl * checking for working pdflatex ... OK * using log directory '/Users/_lzh217/Documents/download/RCurl.Rcheck' * using R version 2.10.0 Under development (unstable) (2009-05-20 r48588) * using session charset: ASCII * checking for file 'RCurl/DESCRIPTION' ... OK * this is package 'RCurl' version '0.97-3' * checking package name space information ... OK * checking package dependencies ... ERROR Packages required but not available: ?Rcompression
Just a quick check--looks like Rcompression is here: http://www.omegahat.org/Rcompression/index.html It also appears that it is not yet mirrored by CRAN. Sean
sessionInfo()
R version 2.10.0 Under development (unstable) (2009-05-20 r48588) i386-apple-darwin8.11.1 locale: [1] 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 other attached packages: [1] multtest_2.1.0 ? ? Biobase_2.5.2 ? ? ?biomaRt_2.1.0 -----Original Message----- From: bioc-devel-bounces at stat.math.ethz.ch on behalf of Julie Zhu Sent: Fri 5/29/2009 11:42 AM To: Florian Hahne Cc: bioc-devel at stat.math.ethz.ch Subject: Re: [Bioc-devel] Need help on biomaRt Florian, Thank you very much for the great news! Best regards, Julie On 5/29/09 11:33 AM, "Florian Hahne" <fhahne at fhcrc.org> wrote:
The problem was fixed by Duncan Temple Lang in the latest RCurl version 0.97-3 which is available from Omegahat (http://www.omegahat.org/RCurl/ ) The automatic updates on our build systems should pick this up any time now, so all you need is patience for one or two more days :) Florian On 28.05.2009, at 11:32, Julie Zhu wrote:
Hi, With the help from Herve, we found out that the devel version of biomaRt is broken with the new Rcurl version 095-1. This is confirmed by the build system: http://bioconductor.org/checkResults/2.5/bioc-LATEST/biomaRt/wilson2-buildsr c.html As you can see, it's broken on Linux and Mac OS. It looks OK on the Window build machine because this machine is using an older version of RCurl (0.94-1). I am in the process of submitting a contributed package that relies on biomaRt and my package won't be passed to the reviewers until biomaRt is fixed. Could someone please fix the devel version of biomaRt? Thanks a lot for your kind help! Best regards, Julie ******************************************* Julie Zhu, Ph.D Research Assistant Professor Program Gene Function and Expression University of Massachusetts Medical School 364 Plantation Street, Room 613 Worcester, MA 01605 http://www.umassmed.edu/pgfe/faculty/zhu.cfm
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
_______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel ? ? ? ?[[alternative HTML version deleted]] _______________________________________________ Bioc-devel at stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel