[BioC] Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't install it because of RCurl)

Wed Sep 17 10:42:32 CEST 2008

On Wed, Sep 17, 2008 at 2:13 AM, Emmanuel Levy <emmanuel.levy at gmail.com> wrote:
> Dear list members,
>
> I'd like to carry out a GO TERM enrichment analysis based on ENSEMBL
> IDs and the GOstats package.
>
> Though I have problems installing biomaRt, which I reported to the R
> mailing list, I was wondering how to use GOstats with biomaRt, i.e.,
> what should be specified for the "annotation package"?
>
> Also, I was wondering if by any chance, somebody could think of a way
> around biomaRt if I can't manage to install it.
>
> Many thanks for your help,
>
> Best wishes,
>
> Emmanuel
>
>
> ==========================================
> Email sent to the R mailing list:
>
> Subject: RCurl compilation error on ubuntu hardy
>
> Dear list members,
>
> I encountered this problem and the solution pointed out in a previous
> thread did not work for me.
> (e.g.  install.packages("RCurl", repos = "http://www.omegahat.org/R")
>
> I work with Ubuntu Hardy, and installed R 2.6.2 via apt-get.
>
> I really need RCurl in order to use biomaRt ... any help would be
> greatly appreciated.

Hi, Emmanuel.  What happened when you upgraded R and tried to install
the newest version of RCurl?  Did that make a difference?

Sean

> =================================================
>
>> sessionInfo()
> R version 2.6.2 (2008-02-08)
> x86_64-pc-linux-gnu
>
> locale:
> LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_COLLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_CA.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-17 tools_2.6.2
>>
>
> =================================================
>
>
>> install.packages("RCurl", repos = "http://www.omegahat.org/R")
> Warning in install.packages("RCurl", repos = "http://www.omegahat.org/R") :
>  argument 'lib' is missing: using '/usr/local/lib/R/site-library'
> trying URL 'http://www.omegahat.org/R/src/contrib/RCurl_0.9-4.tar.gz'
> Content type 'application/x-gzip' length 150884 bytes (147 Kb)
> opened URL
> ==================================================
> downloaded 147 Kb
>
> * 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
> configure: creating ./config.status
> config.status: creating src/Makevars
> ** libs
> gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include
> -DHAVE_LIBIDN_FIELD=1     -fpic  -g -O2 -c base64.c -o base64.o
> In file included from base64.c:1:
> Rcurl.h:52: error: expected specifier-qualifier-list before 'cetype_t'
> make: *** [base64.o] Error 1
> chmod: cannot access `/usr/local/lib/R/site-library/RCurl/libs/*': No
> such file or directory
> ERROR: compilation failed for package 'RCurl'
> ** Removing '/usr/local/lib/R/site-library/RCurl'
>
> The downloaded packages are in
>       /tmp/RtmpQ8FMBZ/downloaded_packages
> Warning message:
> In install.packages("RCurl", repos = "http://www.omegahat.org/R") :
>  installation of package 'RCurl' had non-zero exit status
>
> ================================================================================
>
> Hi Martin,
> are you working on a 64-bit linux distribution and which version of
> RCurl are you trying to install? There has been a problem with a
> recent version of RCurl and the "R_base64_decode", search the archives
> of the Bioconductor mailing list for a thread called
> "RCurl loading problem with 64 bit linux distribution".
> Please try using the newest versions of R (R-2.7.0 has been released a
> few weeks ago) and RCurl, which you can obtain from within R by
> typing:
> install.packages("RCurl", repos = "http://www.omegahat.org/R")
> The new version of RCurl (>= 0.9.2) worked fine for me, while 0.9.0
> and 0.9.1 did not.
> Hope this helps.
> Joern
>
>
> martin sikora wrote:
>
>   dear list members,
>
>   i'm having a problem installing the biomaRt package on my linux
> machine, due to the fact of a compilation error with RCurl. i am using
> R 2.6.2 on fedora 7, and this is the output i get:
>
>   gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R
> -DHAVE_LIBIDN_FIELD=1 -I/usr/local/include    -fpic  -O2 -g -pipe
> -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic
> -fasynchronous-unwind-tables -c base64.c -o base64.o
>   In file included from base64.c:1:
>   Rcurl.h:52: error: expected specifier-qualifier-list before ?cetype_t?
>   base64.c: In function ?R_base64_decode?:
>   base64.c:25: warning: pointer targets in assignment differ in signedness
>   base64.c:39: warning: pointer targets in passing argument 1 of
> ?Rf_mkString? differ in signedness
>   base64.c: In function ?R_base64_encode?:
>   base64.c:60: warning: pointer targets in assignment differ in signedness
>   make: *** [base64.o] Error 1
>
>   as far as i know i have all the necessary libraries installed:
>
>   $ yum list installed | grep libxml
>   libxml2.i386                             2.6.31-1.fc7
> installed      libxml2-devel.i386                       2.6.31-1.fc7
>       installed      libxml2-python.i386
> 2.6.31-1.fc7           installed      perl-libxml-perl.noarch
>       0.08-1.2.1             installed
>   $ yum list installed | grep curl
>   curl.i386                                7.16.4-1.fc7
> installed      curl-devel.i386                          7.16.4-1.fc7
>       installed      python-pycurl.i386
> 7.16.0-0.1.20061207.fc installed
>
>   as i am not an expert in linux stuff, i was wondering if there
> could be any other missing libraries? any other ideas?
>
>   cheers
>   martin
>
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