Ftp Proxy Error in GEO query
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@sailu-yellaboina-3686
Last seen 7.1 years ago
Hi Friends I am getting the following error in using the GEOquery. Funny thing is some times it does not show any error with the same dataset. There was a discussion about this error here < https://stat.ethz.ch/pipermail/bioconductor/2007-December/020471.html > . I want to known if there is any alternative solution is there for this problem (changing the code). I am able to download the dataset ( ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_serie s_matrix.txt.gz) using the wget. dataset.name<-'GSE8024' gse<- getGEOdataset.name, destdir=".") Found 1 file(s) GSE8024_series_matrix.txt.gz trying URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_serie s_matrix.txt.gz ' Error in download.file(sprintf(" ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/%s/%s", : cannot open URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_serie s_matrix.txt.gz ' Calls: getGEO -> getAndParseGSEMatrices -> download.file Execution halted Thank You Sailu Yellaboina Visiting Fellow NIH, NIEHS [[alternative HTML version deleted]]
GEOquery GEOquery • 1.3k views
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@sean-davis-490
Last seen 24 days ago
United States
On Fri, Sep 18, 2009 at 11:20 AM, Sailu Yellaboina <yellaboinas@gmail.com>wrote: > Hi Friends > I am getting the following error in using the GEOquery. Funny thing is > some > times it does not show any error with the same dataset. There was a > discussion about > this error here < > https://stat.ethz.ch/pipermail/bioconductor/2007-December/020471.html > . > I > want to known if there is any alternative solution is there for this > problem > (changing the code). I am able to download the dataset ( > > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_ser ies_matrix.txt.gz > ) > using the wget. > > dataset.name<-'GSE8024' > gse<- getGEOdataset.name, destdir=".") > Found 1 file(s) > GSE8024_series_matrix.txt.gz > trying URL ' > > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_ser ies_matrix.txt.gz > ' > Error in download.file(sprintf(" > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/%s/%s", : > cannot open URL ' > > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_ser ies_matrix.txt.gz > ' > Calls: getGEO -> getAndParseGSEMatrices -> download.file > Execution halted > > Hi, Sailu. This is not a GEOquery problem or a problem with anything locally, I don't think. The FTP server at NCBI is sometimes busy and doesn't accept the connection. If you try your query later, it will likely work. You could also use a loop wrapped around a "try" command something like what is shown below: Hope this helps. Sean ----------------------------- loopGetGEO <- function(...) { returnGEO <- NULL notdone <- TRUE while(notdone) { returnGEO <- try(getGEO(...)) if(!inherits(returnGEO,"try-error")) notdone <- FALSE else cat("Caught an error in getGEO, so trying again....\n") } return(returnGEO) } > gse <- loopGetGEO("GSE8024") Found 1 file(s) GSE8024_series_matrix.txt.gz trying URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_serie s_matrix.txt.gz ' Error in download.file(sprintf(" ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/%s/%s", : cannot open URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_serie s_matrix.txt.gz ' Caught an error in getGEO, so trying again.... Found 1 file(s) GSE8024_series_matrix.txt.gz trying URL ' ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE8024/GSE8024_serie s_matrix.txt.gz ' ftp data connection made, file length 1520554 bytes opened URL ================================================== downloaded 1.5 Mb [[alternative HTML version deleted]]
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