Question: GEOquery -> cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/ ....
0
gravatar for Manca Marco PATH
8.8 years ago by
Manca Marco PATH340 wrote:
Dear Sean, dear BioConductors I am having some troubles using GEOquery. In fact, it won't connect to the GEO to download any data... I have tried even with datasets from the vignette and the result is the same. The website is working though (I can access the data if I use a browser i.e.: Firefox3.6.13) and my R can currently connect, as I have no problem using KEGGSOAP as instance. Any suggestion? I am attaching my "code" and sessionInfo(). Thank you in advance and best regards, Marco #####@Workstation1:~$ R R version 2.12.1 (2010-12-16) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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)'. > gds <- getGEO("GDS1") Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) : cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz' > gse <- getGEO("GSE462") Found 1 file(s) GSE462_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE462/GS E462_series_matrix.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/GS E462/GSE462_series_matrix.txt.gz' > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.16.3 Biobase_2.10.0 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.2-0 > -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confide...{{dropped:15}}
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ADD COMMENTlink modified 8.8 years ago by Sean Davis21k • written 8.8 years ago by Manca Marco PATH340
Answer: GEOquery -> cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/ .
0
gravatar for Sean Davis
8.8 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Tue, Feb 8, 2011 at 9:18 AM, Manca Marco (PATH) < m.manca@maastrichtuniversity.nl> wrote: > > Dear Sean, dear BioConductors > > I am having some troubles using GEOquery. In fact, it won't connect to the > GEO to download any data... I have tried even with datasets from the > vignette and the result is the same. The website is working though (I can > access the data if I use a browser i.e.: Firefox3.6.13) and my R can > currently connect, as I have no problem using KEGGSOAP as instance. > > Any suggestion? I am attaching my "code" and sessionInfo(). > > Hi, Marco. Try: options('download.file.method'='curl') This is related to an issue between the internal download.file method under linux and the NCBI ftp servers. Sean > Thank you in advance and best regards, > Marco > > > #####@Workstation1:~$ R > > R version 2.12.1 (2010-12-16) > Copyright (C) 2010 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > > 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)'. > > > gds <- getGEO("GDS1") > Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) : > cannot open URL ' > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz' > > gse <- getGEO("GSE462") > Found 1 file(s) > GSE462_series_matrix.txt.gz > trying URL ' > ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE462/GSE462_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/GSE462/GSE462_serie s_matrix.txt.gz > ' > > > sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-pc-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 > [7] LC_PAPER=en_US.utf8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GEOquery_2.16.3 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] RCurl_1.5-0 XML_3.2-0 > > > > > > -- > Marco Manca, MD > University of Maastricht > Faculty of Health, Medicine and Life Sciences (FHML) > Cardiovascular Research Institute (CARIM) > > Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) > Visiting address: Experimental Vascular Pathology group, Dept of Pathology > - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX > Maastricht > > E-mail: m.manca@maastrichtuniversity.nl > Office telephone: +31(0)433874633 > Personal mobile: +31(0)626441205 > Twitter: @markomanka > > > > ******************************************************************** ************************************************* > > This email and any files transmitted with it are confide...{{dropped:15}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 8.8 years ago by Sean Davis21k
Dear Sean, thank you for your prompt reply. It works like a charm once options('download.file.method'='curl') as you suggested. All the best, Marco -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confidential and solely for the use of the intended recipient. It may contain material protected by privacy or attorney-client privilege. If you are not the intended recipient or the person responsible for delivering to the intended recipient, be advised that you have received this email in error and that any use is STRICTLY PROHIBITED. If you have received this email in error please notify us by telephone on +31626441205 Dr Marco MANCA ********************************************************************** *********************************************** ________________________________________ Da: seandavi at gmail.com [seandavi at gmail.com] per conto di Sean Davis [sdavis2 at mail.nih.gov] Inviato: marted? 8 febbraio 2011 15.29 A: Manca Marco (PATH) Cc: bioconductor mailing list Oggetto: Re: [BioC] GEOquery -> cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/ .... On Tue, Feb 8, 2011 at 9:18 AM, Manca Marco (PATH) <m.manca at="" maastrichtuniversity.nl<mailto:m.manca="" at="" maastrichtuniversity.nl="">> wrote: Dear Sean, dear BioConductors I am having some troubles using GEOquery. In fact, it won't connect to the GEO to download any data... I have tried even with datasets from the vignette and the result is the same. The website is working though (I can access the data if I use a browser i.e.: Firefox3.6.13) and my R can currently connect, as I have no problem using KEGGSOAP as instance. Any suggestion? I am attaching my "code" and sessionInfo(). Hi, Marco. Try: options('download.file.method'='curl') This is related to an issue between the internal download.file method under linux and the NCBI ftp servers. Sean Thank you in advance and best regards, Marco #####@Workstation1:~$ R R version 2.12.1 (2010-12-16) Copyright (C) 2010 The R Foundation for Statistical Computing ISBN 3-900051-07-0 Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > 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)'. > gds <- getGEO("GDS1") Error in download.file(myurl, destfile, mode = mode, quiet = TRUE) : cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SOFT/GDS/GDS1.soft.gz' > gse <- getGEO("GSE462") Found 1 file(s) GSE462_series_matrix.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE462/GS E462_series_matrix.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/GSE 462/GSE462_series_matrix.txt.gz' > sessionInfo() R version 2.12.1 (2010-12-16) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=C LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GEOquery_2.16.3 Biobase_2.10.0 loaded via a namespace (and not attached): [1] RCurl_1.5-0 XML_3.2-0 > -- Marco Manca, MD University of Maastricht Faculty of Health, Medicine and Life Sciences (FHML) Cardiovascular Research Institute (CARIM) Mailing address: PO Box 616, 6200 MD Maastricht (The Netherlands) Visiting address: Experimental Vascular Pathology group, Dept of Pathology - Room5.08, Maastricht University Medical Center, P. Debyelaan 25, 6229 HX Maastricht E-mail: m.manca at maastrichtuniversity.nl<mailto:m.manca at="" maastrichtuniversity.nl=""> Office telephone: +31(0)433874633 Personal mobile: +31(0)626441205 Twitter: @markomanka ********************************************************************** *********************************************** This email and any files transmitted with it are confide...{{dropped:15}} _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org<mailto:bioconductor at="" r-project.org=""> https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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