[BioC] Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't install it because of RCurl)
Robert Gentleman
rgentlem at fhcrc.org
Wed Sep 17 14:48:29 CEST 2008
Hi Emmanuel,
Emmanuel Levy wrote:
> Dear list members,
>
> I'd like to carry out a GO TERM enrichment analysis based on ENSEMBL
> IDs and the GOstats package.
That depends a bit on the organism you are wanting to use. For those
that are supported by the org.xx.yy.db packages, such as human,
org.Hs.eg
there are maps in those annotation packages
[9] "org.Hs.egENSEMBL2EG" "org.Hs.egENSEMBLPROT"
[11] "org.Hs.egENSEMBLPROT2EG" "org.Hs.egENSEMBLTRANS"
[13] "org.Hs.egENSEMBLTRANS2EG" "org.Hs.egENZYME"
the hardest part, in any of this is typically not the map from one
type of identifier to another, but rather correctly identifying the gene
universe (those genes that could have been selected), as that usually
has a bigger effect on the p-values (and inference) than anything.
>
> 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"?
I think that that discussion suggested an upgrade of R (which you
will need for the tools I have described as well).
best wishes
Robert
>
> 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.
>
> Best wishes,
>
> Emmanuel
>
> =================================================
>
>> 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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--
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org
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