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

Thu Sep 18 02:25:18 CEST 2008

Dear Sean,

That was indeed the issue. I tried to upgrade R yesterday but it
didn't work and I had
(i) to add a CRAN mirror to the list of Ubuntu package repositories.
(ii) use aptitude instead of apt-get because apt-get held back the
update for some reason.

I'm happy to say that the issue is now fixed!

Many thanks,

Best wishes,

Emmanuel

2008/9/17 Sean Davis <sdavis2 at mail.nih.gov>:
> 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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>