Hi, I'm having trouble getting GEOquery to work recently. On Ubuntu 9.10/R-2.10.1/BioC 2.6.1, GEOquery 2.11.3, download.file stops with "cannot open URL", On Ubuntu 8.04.1/R-2.9.2/BioC 2.4.1, GEOquery 2.8.0, curlPerform stops with "Server denied you to change to the given directory" wget downloads the file fine, but requires PASV which download.file() doesn't support (http://tolstoy.newcastle.edu.au/R/e6/help/09/01/0969.html) I suspect that NCBI has changes some server settings, is this a known issue? Thanks, Gad > library(GEOquery) Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RCurl Loading required package: bitops > g <- getGEO("GSE2034") Found 2 file(s) GSE2034_series_matrix-1.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/G SE2034_series_matrix-1.txt.gz' Error in download.file(sprintf("ftp://ftp.ncbi.nih.gov/pub/geo/DATA/Se riesMatrix/%s/%s", : cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE2034_seri es_matrix-1.txt.gz' > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_AU.UTF-8 [7] LC_PAPER=en_AU.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.11.3 RCurl_1.3-1 bitops_1.0-4.1 Biobase_2.6.1 $ wget ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE203 4_series_matrix-1.txt.gz --2010-03-03 22:08:59-- ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE2034_serie s_matrix-1.txt.gz => `GSE2034_series_matrix-1.txt.gz' Resolving ftp.ncbi.nih.gov... 130.14.29.30 Connecting to ftp.ncbi.nih.gov|130.14.29.30|:21... connected. Logging in as anonymous ... Logged in! ==> SYST ... done. ==> PWD ... done. ==> TYPE I ... done. ==> CWD /pub/geo/DATA/SeriesMatrix/GSE2034 ... done. ==> SIZE GSE2034_series_matrix-1.txt.gz ... 12800217 ==> PASV ... done. ==> RETR GSE2034_series_matrix-1.txt.gz ... done. Length: 12800217 (12M) etc. -- Gad Abraham PhD Student, Dept. CSSE and NICTA The University of Melbourne Parkville 3010, Victoria, Australia email: gabraham at csse.unimelb.edu.au web: http://www.csse.unimelb.edu.au/~gabraham

On Wed, Mar 3, 2010 at 6:32 AM, Gad Abraham <gabraham at="" csse.unimelb.edu.au=""> wrote: > Hi, > > I'm having trouble getting GEOquery to work recently. > > On Ubuntu 9.10/R-2.10.1/BioC 2.6.1, GEOquery 2.11.3, download.file > stops with "cannot open URL", > On Ubuntu 8.04.1/R-2.9.2/BioC 2.4.1, GEOquery 2.8.0, curlPerform stops > with "Server denied you to change to the given directory" > > wget downloads the file fine, but requires PASV which download.file() > doesn't support > (http://tolstoy.newcastle.edu.au/R/e6/help/09/01/0969.html) > > I suspect that NCBI has changes some server settings, is this a known issue? Hi, Gad. I'll follow up with the GEO folks, but it appears that the issue was temporary. I was able to reproduce your findings for until 7am EST and then the problem was gone. Currently, GEOquery appears to work fine for me. Let me know if you are still having problems. Sean >> library(GEOquery) > Loading required package: Biobase > > Welcome to Bioconductor > > ?Vignettes contain introductory material. To view, type > ?'openVignette()'. To cite Bioconductor, see > ?'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: RCurl > Loading required package: bitops >> g <- getGEO("GSE2034") > Found 2 file(s) > GSE2034_series_matrix-1.txt.gz > trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034 /GSE2034_series_matrix-1.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/GSE2034/GSE2034_se ries_matrix-1.txt.gz' >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > > locale: > ?[1] LC_CTYPE=en_AU.UTF-8 ? ? ? LC_NUMERIC=C > ?[3] LC_TIME=en_AU.UTF-8 ? ? ? ?LC_COLLATE=en_AU.UTF-8 > ?[5] LC_MONETARY=C ? ? ? ? ? ? ?LC_MESSAGES=en_AU.UTF-8 > ?[7] LC_PAPER=en_AU.UTF-8 ? ? ? LC_NAME=C > ?[9] LC_ADDRESS=C ? ? ? ? ? ? ? LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] GEOquery_2.11.3 RCurl_1.3-1 ? ? bitops_1.0-4.1 ?Biobase_2.6.1 > > > $ wget ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE2 034_series_matrix-1.txt.gz > --2010-03-03 22:08:59-- > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2034/GSE2034_ser ies_matrix-1.txt.gz > ? ? ? ? ? => `GSE2034_series_matrix-1.txt.gz' > Resolving ftp.ncbi.nih.gov... 130.14.29.30 > Connecting to ftp.ncbi.nih.gov|130.14.29.30|:21... connected. > Logging in as anonymous ... Logged in! > ==> SYST ... done. ? ?==> PWD ... done. > ==> TYPE I ... done. ?==> CWD /pub/geo/DATA/SeriesMatrix/GSE2034 ... done. > ==> SIZE GSE2034_series_matrix-1.txt.gz ... 12800217 > ==> PASV ... done. ? ?==> RETR GSE2034_series_matrix-1.txt.gz ... done. > Length: 12800217 (12M) > etc. > > -- > Gad Abraham > PhD Student, Dept. CSSE and NICTA > The University of Melbourne > Parkville 3010, Victoria, Australia > email: gabraham at csse.unimelb.edu.au > web: http://www.csse.unimelb.edu.au/~gabraham > > _______________________________________________ > 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 >