[Bioc-devel] Need help on biomaRt

Tue Jun 2 19:50:19 CEST 2009

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
>>
>>
>
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