[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
Fri Sep 19 00:26:36 CEST 2008
Dear Robert,
>> I agree, yet if you type in google:
>> site:www.bioconductor.org gostats org.Hs.eg.db
>
> Well, I guess my point was that google is not a particularly useful tool
> for finding documentation for Bioconductor (or indeed most R) packages. They
> have documentation that comes with them, and that should be the first place
> you look.
Yes - I unfortunately came to this conclusion several times but I
guess I'm too conditioned now.
>> 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.
Sorry for asking the same question again, would it be that stupid? Do
I have to create an environment myself that maps human IDs to GO IDs,
in a similar way as it is done in the YEAST environment?
Many thanks,
Emmanuel
>>
>> 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
>>>
>>
>
> --
> 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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