Ensembl IDs 2 GO term enrichment --> simple solution withoutbiomart? ( I can't install it because of RCurl)
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@michael-watson-iah-c-378
Last seen 9.6 years ago
www.fatigo.org Paste ensembl ids into the box :) -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Emmanuel Levy Sent: Wed 17/09/2008 7:13 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Ensembl IDs 2 GO term enrichment --> simple solution withoutbiomart? ( I can't install it because of RCurl) 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. 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
GO GOstats biomaRt GO GOstats biomaRt • 911 views
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@michael-watson-iah-c-378
Last seen 9.6 years ago
If you are stuck on using R, then biomart is simply a web service. To link ens genes to affy chicken, the url is: http://www.biomart.org/biomart/martservice?query=%3C?xml%20version=%22 1.0%22%20encoding=%22UTF-8%22?%3E%3C!DOCTYPE%20Query%3E%3CQuery%20%20v irtualSchemaName%20=%20%22default%22%20formatter%20=%20%22TSV%22%20hea der%20=%20%220%22%20uniqueRows%20=%20%220%22%20count%20=%20%22%22%20da tasetConfigVersion%20=%20%220.6%22%20%3E%3CDataset%20name%20=%20%22gga llus_gene_ensembl%22%20interface%20=%20%22default%22%20%3E%3CAttribute %20name%20=%20%22ensembl_gene_id%22%20/%3E%3CAttribute%20name%20=%20%2 2affy_chicken%22%20/%3E%3C/Dataset%3E%3C/Query%3E thats how my browser formatted it, but I pasted: http://www.biomart.org/biomart/martservice?query=<query virtualschemaname="default" formatter="TSV" header="0" uniquerows="0" count="" datasetconfigversion="0.6"><dataset name="ggallus_gene_ensembl" interface="default"><attribute name="ensembl_gene_id"/><attribute name="affy_chicken"/></dataset></query> In R, I can do this: url <- 'http://www.biomart.org/biomart/martservice?query=%3C?xml%20ver sion=%221.0%22%20encoding=%22UTF-8%22?%3E%3C!DOCTYPE%20Query%3E%3CQuer y%20%20virtualSchemaName%20=%20%22default%22%20formatter%20=%20%22TSV% 22%20header%20=%20%220%22%20uniqueRows%20=%20%220%22%20count%20=%20%22 %22%20datasetConfigVersion%20=%20%220.6%22%20%3E%3CDataset%20name%20=% 20%22ggallus_gene_ensembl%22%20interface%20=%20%22default%22%20%3E%3CA ttribute%20name%20=%20%22ensembl_gene_id%22%20/%3E%3CAttribute%20name% 20=%20%22affy_chicken%22%20/%3E%3C/Dataset%3E%3C/Query%3E' d <- read.table(url, sep="\t") d[1:5,] V1 V2 1 ENSGALG00000014600 2 ENSGALG00000011014 Gga.9239.1.S1_s_at 3 ENSGALG00000011014 Gga.16267.1.S1_at 4 ENSGALG00000011014 Gga.9239.1.S1_s_at 5 ENSGALG00000011014 Gga.16267.1.S1_s_at Mick -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch on behalf of Emmanuel Levy Sent: Wed 17/09/2008 7:13 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] Ensembl IDs 2 GO term enrichment --> simple solution withoutbiomart? ( I can't install it because of RCurl) 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. 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
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