[BioC] Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't install it because of RCurl)
Emmanuel Levy
emmanuel.levy at gmail.com
Thu Sep 18 22:57:25 CEST 2008
Dear Robert,
Thank you for your reply.
> That seems like an odd place to look for help on Bioconductor packages
> (usually the URL would start a bit more like www.bioconductor.org).
I agree, yet if you type in google:
site:www.bioconductor.org gostats org.Hs.eg.db
It seems that there is no example on how to use it.
> library(org.Hs.eg.db)
> ls(2) #as one variant
Great thanks! I didn't known that trick.
>> Finally, I googled for the keywords "GOstats and biomart" and did not
>> find any page that shows how to use them together. (In fact my post
>> from yesterday appears in 3rd position!)
>> Is it so straightforward to use them together and I'm being slow? Or
>> are they incompatible?
>
> They are not incompatible, but as I said in my previous email, the issue of
> how to determine the universe is not simple.
In my case, to determine the universe is OK (or so I think): I am
looking at a particular property among all proteins with a
charaterized phosphorilation site (which is my universe). So I've got
two lists of IDs, one of the universe and one of a subset of proteins
with a particular trait. However I'm just not sure which parameter to
give for the annotation package.
Any hint would be greatly appreciated!
Many thanks,
Emmanuel
>
> best wishes
> Robert
>
>>
>> Thanks again for your help!
>>
>> Best wishes,
>>
>> Emmanuel
>>
>>
>>>> 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
>>>>
>>>> _______________________________________________
>>>> Bioconductor mailing list
>>>> Bioconductor at stat.math.ethz.ch
>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>> Search the archives:
>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>
>>> --
>>> 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
>>>
>>
>
> --
> 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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