Amy Mikhail wrote: > Hi Jim, > > If I try that I get the same error: > > >>library(biomaRt) > > Loading required package: XML > Loading required package: RCurl > > >>example(postForm) > > > pstFrm> > getURL("http://www.google.com/search?hl=en&lr=&ie=ISO-8859-1&q=RCurl &btnG=Search") > Error in curlPerform(curl = curl, .opts = opts) : > couldn't connect to host > > So would that be a firewall? If so what should I do to get round it? I don't know if it is a firewall or not - I don't have a problem with ours, so I have no experience. However, try adding --internet2 to the target for your R shortcut, and see if you can run the postForm() example. If you really are having firewall problems, that may help (I know it is supposed to help with download.packages(), so it may well help here). If it doesn't help, then Duncan Temple Lang is probably the person to ask. He is the RCurl maintainer, so is the most likely person to have experience with this problem. Anyway, in my experience the RMySQL interface is faster, so if you have RMySQL installed, you can just add mysql = TRUE to your call to useMart() and all these problems will then be moot. Best, Jim > > Cheers, > Amy > -------------------------------------------------------------------- ------- > >>Amy Mikhail wrote: >> >>>Dear list, >>> >>>I have downloaded R 2.3 and bioconductor 1.8 devel but can't get the >>>useMart function to work... is this the connection error Wolfgang was >>>referring to earlier? Here's my code: >>> >>>library(biomaRt) >>>Loading required package: XML >>>Loading required package: RCurl >>> >>> >>>>mart <- useMart("ensembl_mart_37") >>> >>>Error in curlPerform(curl = curl, .opts = opts) : >>> couldn't connect to host >> >>That is an odd error. AFAIK, you should just get an error saying you are >> using the wrong name: >> >> > mart <- useMart("ensembl_mart_37") >>Error in useMart("ensembl_mart_37") : Incorrect biomart name >> > mart <- useMart("ensembl") >> > mart >>An object of class "Mart" >>Slot "mysql": >>[1] FALSE >> >>Slot "connections": >>list() >> >>Slot "mysqldriver": >>list() >> >>Slot "mainTables": >>list() >> >>Slot "biomart": >>[1] "ensembl" >> >>Slot "host": >>[1] "http://www.biomart.org/biomart/martservice" >> >>Slot "dataset": >>[1] "" >> >>Slot "filters": >><environment: 01abfedc=""> >> >>Slot "attributes": >><environment: 0219950c=""> >> >> > sessionInfo() >>Version 2.3.0 Under development (unstable) (2006-02-17 r37375) >>i386-pc-mingw32 >> >>attached base packages: >>[1] "methods" "stats" "graphics" "grDevices" "utils" >>"datasets" "base" >> >>other attached packages: >> biomaRt RCurl XML >>"1.5.12" "0.6-0" "0.99-6" >> >>> >>>If I try it the old way, this is what I get: >>> >>> mart <- martConnect() >>> >>>############################################### >>> >>>This function will go out of use soon, please adapt by using the >>>'useMart' >>>function instead. >>> >>>############################################### >>> >>>Loading required package: RMySQL >>>Loading required package: DBI >>>connected to: ensembl_mart_37 >>>Warning message: >>>DLL attempted to change FPU control word from 8001f to 9001f >>> >>>Nb. I have found posts in the archive with the same warning message as >>>above (relating to the control word) but did not find any suggestions >>>as >>>to what to do about it. >>> >>>Should I be worrying about this warning? >>> >>>I can chose the species as follows: >>> >>> >>> >>>>listDatasets(mart) >>> >>> dataset version >>>1 agambiae_gene_ensembl AgamP3 >>>2 amellifera_gene_ensembl AMEL2.0 >>>3 btaurus_gene_ensembl Btau_2.0 >>>4 cfamiliaris_gene_ensembl BROADD1 >>>5 cintestinalis_gene_ensembl JGI2 >>>6 dmelanogaster_gene_ensembl BDGP4 >>>7 drerio_gene_ensembl ZFISH5 >>>8 frubripes_gene_ensembl FUGU4 >>>9 ggallus_gene_ensembl WASHUC1 >>>10 hsapiens_gene_ensembl NCBI35 >>>11 mdomestica_gene_ensembl BROADO2 >>>12 mmulatta_gene_ensembl MMUL_0_1 >>>13 mmusculus_gene_ensembl NCBIM34 >>>14 ptroglodytes_gene_ensembl CHIMP1A >>>15 rnorvegicus_gene_ensembl RGSC3.4 >>>16 scerevisiae_gene_ensembl SGD1 >>>17 tnigroviridis_gene_ensembl TETRAODON7 >>>18 xtropicalis_gene_ensembl JGI4 >>>19 celegans_gene_ensembl CEL150 >>> >>> >>>>mart <- useDataset(dataset = "agambiae_gene_ensembl", mart = mart) >>> >>>Reading database configuration of: agambiae_gene_ensembl >>>Checking main tables ... ok >>>Checking attributes and filters ... ok >>> >>>On the other hand if I try specifying the species with useMart this is >>>what happens: >>> >>> >>> >>>>mart <- useMart("ensembl", dataset = "agambiae_gene_ensembl") >>> >>>Error in curlPerform(curl = curl, .opts = opts) : >>> couldn't connect to host >> >>Odd. I get that to work. >> >> > mart <- useMart("ensembl", dataset = "agambiae_gene_ensembl") >>Checking attributes and filters ... ok >> >> >>>So it seems like RCurl is not working and biomaRt is still using RMySQL? >>>Why would useMart not work? >> >>biomaRt *can* still use RMySQL, but the default is to use RCurl because >>RMySQL can be a pain for win32 users to install. >> >> >>>Looking forward to any suggestions, >> >>I'm wondering if you are behind a firewall and that is causing problems >>with RCurl. Can you get e.g., example(postForm) to work? >> >>Best, >> >>Jim >> >> >> >>>Regards, >>>Amy >>> >>>P.s. appologies if this should have been posted to the devel list - I >>>just >>>suppose that if everyone is using the devel version of biomaRt it would >>>be >>>appropriate here. >>> >>> >>> >>>>sessionInfo() >>> >>>Version 2.3.0 alpha (2006-03-27 r37590) >>>i386-pc-mingw32 >>> >>>attached base packages: >>>[1] "methods" "stats" "graphics" "grDevices" "utils" >>>"datasets" >>>[7] "base" >>> >>>other attached packages: >>> RMySQL DBI biomaRt RCurl XML >>> "0.5-6" "0.1-10" "1.5.12" "0.6-0" "0.99-6" >>> >>> >>> >>>------------------------------------------- >>>Amy Mikhail >>>Research student >>>University of Aberdeen >>>Zoology Building >>>Tillydrone Avenue >>>Aberdeen AB24 2TZ >>>Scotland >>>Email: a.mikhail at abdn.ac.uk >>>Phone: 00-44-1224-272880 (lab) >>> >>>_______________________________________________ >>>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 >> >> >>-- >>James W. MacDonald, M.S. >>Biostatistician >>Affymetrix and cDNA Microarray Core >>University of Michigan Cancer Center >>1500 E. Medical Center Drive >>7410 CCGC >>Ann Arbor MI 48109 >>734-647-5623 >> >> >>********************************************************** >>Electronic Mail is not secure, may not be read every day, and should not >>be used for urgent or sensitive issues. >> > > > > ------------------------------------------- > Amy Mikhail > Research student > University of Aberdeen > Zoology Building > Tillydrone Avenue > Aberdeen AB24 2TZ > Scotland > Email: a.mikhail at abdn.ac.uk > Phone: 00-44-1224-272880 (lab) > > -- James W. MacDonald, M.S. Biostatistician Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.