similar to: reading tables from url

Hi, > url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" > download.file(url, tempfile()) trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' Error in download.file(url, tempfile()) : cannot open URL

----- Original Message ----- > From: "Uwe Ligges" <ligges at statistik.tu-dortmund.de> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "R-devel at r-project.org" <r-devel at r-project.org> > Sent: Saturday, August 8, 2015 3:57:34 PM > Subject: Re: [Rd] download.file() on ftp URL fails in windows with default download method > >

We were also able to reproduce the issue on Windows Server 2012. If there's anything we can do to help please let me know; Elliot Waingold (CC'd here) can provide access to the VM we used for testing if that's of any help. # David Smith -- David M Smith <davidsmi at microsoft.com> R Community Lead, Revolution Analytics (a Microsoft company)? Tel: +1 (312) 9205766 (Chicago IL,

I wrote a package which includes a number of genome sequencing project statistics on the web like http://www.ncbi.nlm.nih.gov/genomes/lproks.cgi. I included some generic functions to summarize, plot, and update the tables with the most recent version data(lproks) update(lproks) [1] "lproks successfully updated, 7 new genomes added" I usually save the dataset back to my package

Hi all, I''m working with a legacy sqlserver db and I''m trying to override the insert sql in as defined in the HABTM method below(becasue the join has three primary keys), but I''m getting the error: ''undefined local variable or method `record'' for Project:Class'' has_and_belongs_to_many :people, :class => ''Person'',

Hello! I am crossposting this to R-help and BioC, since it is relevant to both groups. I wrote a wrapper for Entrez search utility (link for this is provided bellow), which can add some new search functionality to existing code in Bioconductor's package 'annotate'*. http://eutils.ncbi.nlm.nih.gov/entrez/query/static/esearch_help.html Entrez search utuility returns a XML document

Hi, Trying to access files on the ftp server at ftp.ncbi.nih.gov will either give a time out or sometimes even a segfault on Linux. The 2 following methods give the same results: f <- url("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", open="r") download.file("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS10.soft.gz", destfile=tempfile())

Hi, I am trying to use a CGI service (Pubchem PUG) via RCurl and am running into a problem where the data must be supplied via POST - but I don't know the keyword for the argument. The data to be sent is an XML fragment. I can do this via the command line using curl: I save the XML string to a file called query.xml and then do curl -d @query.xml

On 08.08.2015 01:11, Dan Tenenbaum wrote: > Hi, > >> url <- "ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt" >> download.file(url, tempfile()) > trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/All/GCF_000001405.13.assembly.txt' > Error in download.file(url, tempfile()) : > cannot open URL

Hi David, ----- Original Message ----- > From: "David Smith" <davidsmi at microsoft.com> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "Uwe Ligges" <ligges at statistik.tu-dortmund.de>, "Elliot Waingold" > <Elliot.Waingold at microsoft.com> > Cc: "R-devel at r-project.org" <r-devel at r-project.org>

----- Original Message ----- > From: "Dan Tenenbaum" <dtenenba at fredhutch.org> > To: "Uwe Ligges" <ligges at statistik.tu-dortmund.de> > Cc: "R-devel at r-project.org" <r-devel at r-project.org> > Sent: Saturday, August 8, 2015 4:02:54 PM > Subject: Re: [Rd] download.file() on ftp URL fails in windows with default download method

(Mostly for Roy): I saw this on the SWIG list, and wonder if it might be related to the problems we have been seeing where multi-arg typemaps end up invoking the wrong wrapper methods. (Not the newly-discovered directorout stuff). Perhaps if we switched to "compactdefaultargs" things would start to work more sanely. Looking at this section of the SWIG docs, it looks like it should

Hi all, I am trying to download, decompress and read a csv file. My code: myurl <- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE24729/GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # myfile <- "GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # download.file(myurl, destfile=myfile, mode="w") # mycon <- gzcon(gzfile(myfile,

Hi, I'm trying to calculate p-value to findout definitely expressed genes compare A to B situation. I got this data(this is a part of data) from whole organism , and each number means each expression values (that means, we could think 'a' gene is 13 in A situation, and it turns 30 in B situation) To findout probability, I'm going to use Audic - Claverie Method. ( The significance

Hi dear Rers, I am using SSOAP package to access SOAP service at NCBI. I followed the example code in SSOAP but failed. > z <- .SOAP("http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/soap_adapter.cgi", method="run_eInfo", db="pubmed", action = I("einfo")) Error: protect(): protection stack overflow what's wrong? Thanks very much. Regards

Hi, I wanted to download a file and did the following: --------------------------------------------------------- > fileLink <- 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' > download.file(fileLink,'/geoDat') trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1000/GSE1000_RAW.tar' ftp data connection made,

for the script, please kindly see the script below. At line 10 and line 13, my problems occurs. The first one is I try to retrieve the gene official name from a column of a table. The pattern of official name is something starting with gene_name. For detail problems, please see the according lines. Any suggestions are appreciated example of matching source (extract the Nnat, sometime it would

Hi all, I'm new to Centos, just moved here from Gentoo Linux. I have to install a server for bioinformatics purposes and I see that default yum repositories do not include any bioinformatics software (i.e. ncbi-toolkit, blat, and others). I'm googling a bit but I can't find a valuable solution: which is (or which are) the best repository I should add to have a satisfying list

hi! I''m migrating to Rails 1.2.1 (from 1.1.6), but now I''m getting a 404 (Not Found) page for every url I call! Not even the error messages I got before are shown on this page anymore. So I took a look into development.log, but there everything is ok, WebRick sends Http 200 OK. The routes.rb I left as the standard: map.connect '':controller/:action/:projectid''

Dear all, I've noticed by trying to download gz files from here : https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM907811 At the bottom one can download GSM907811.CEL.gz . If I download this manually and try oligo::read.celfiles("GSM907811.CEL.gz") everything works fine. (oligo is a bioConductor package) However, if I download using download.file("