Dear Amy, I had the same problem with the biomaRt package before. But now it works fine with the option, *mysql = TRUE*, as Jim suggested. ================================= mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") # Error in curlPerform(curl = curl, .opts = opts) : # Failed writing body mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl", mysql=T) # connected to: ensembl # Reading database configuration of: hsapiens_gene_ensembl # Checking main tables ... ok # Checking attributes and filters ... ok mart <- useMart("ensembl_mart_37") # Error in curlPerform(curl = curl, .opts = opts) : # Failed writing body mart <- useMart("ensembl_mart_37", mysql=T) # connected to: ensembl_mart_37 ================================ Regards, Ho >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=RCu rl&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.conducto r >>> >>> >>>> >>>> >>>>-- >>>>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.