[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
Thu Sep 18 23:54:07 CEST 2008
Emmanuel Levy wrote:
> 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
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.
>
> 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
>>
>
--
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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