After some further testing, it doesn't appear to be an ftp problem directly, and comes down to the getURL() step in getDirectoryListing(): > GEOquery:::getDirListing("ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nn n/GSE9514/matrix/") ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9514/matrix/ Error in function (type, msg, asError = TRUE) : couldn't connect to host But this works with other FTP sites, such as in R's internet test file: > GEOquery:::getDirListing("ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/") ftp://ftp.stats.ox.ac.uk/pub/datasets/csb/ [1] "HEADER.html" "ch10.dat" "ch10.sas" "ch10.txt" "ch11a.dat" "ch11a.sas" "ch11a.txt" "ch11b.dat" [9] "ch11b.sas" "ch11b.txt" "ch12.dat.gz" "ch12.sas" "ch12.txt" "ch13.dat.gz" "ch13.sas" "ch13.txt" [17] "ch14.dat" "ch14.sas" "ch14.txt" "ch15.dat.gz" "ch15.sas" "ch15.txt" "ch16a.dat" "ch16a.sas" [25] "ch16a.txt" "ch16b.dat" "ch16b.sas" "ch16b.txt" "ch17.dat" "ch17.sas" "ch17.txt" "ch18a.dat" [33] "ch18a.sas" "ch18a.txt" "ch18b.dat.gz" "ch18b.sas" "ch18b.txt" "ch19.sas" "ch19.txt" "ch19a.dat.gz" [41] "ch19b.dat.gz" "ch19c.dat.gz" "ch19d.dat.gz" "ch19e.dat.gz" "ch19f.dat.gz" "ch19g.dat.gz" "ch1a.dat" "ch1a.sas" [49] "ch1a.txt" "ch1b.dat" "ch1b.sas" "ch1b.txt" "ch2.dat" "ch2.sas" "ch2.txt" "ch20.dat.gz" [57] "ch20.sas" "ch20.txt" "ch21a.dat.gz" "ch21a.sas" "ch21a.txt" "ch21b.dat.gz" "ch21b.sas" "ch21b.txt" [65] "ch3a.dat" "ch3a.sas" "ch3a.txt" "ch3b.dat" "ch3b.sas" "ch3b.txt" "ch4a.dat" "ch4a.sas" [73] "ch4a.txt" "ch4b.dat" "ch4b.sas" "ch4b.txt" "ch5.dat.gz" "ch5.sas" "ch5.txt" "ch6.dat" [81] "ch6.sas" "ch6.txt" "ch7.dat.gz" "ch7.sas" "ch7.txt" "ch8.dat" "ch8.sas" "ch8.txt" [89] "ch9.dat.gz" "ch9.sas" "ch9.txt" "index.html" or Ensembl: > GEOquery:::getDirListing("ftp://ftp.ensembl.org") ftp://ftp.ensembl.org [1] "ls-lR.gz" "ls-lR.Z" "pub" "quota.group" "quota.user" [6] "update-sym-links" "update-sym-links_orig" or other random US government ftp sites: > GEOquery:::getDirListing("ftp://ftp.wcc.nrcs.usda.gov") ftp://ftp.wcc.nrcs.usda.gov [1] "BB_Test" "data" "downloads" "fieldops" "gis" "images" "pub" "publications" [9] "snowschool" "states" "support" "tmp" "watershed" "wcs_info" "welcome.msg" "wntsc" So I wonder if it is a change at NCBI? Best, Jim On 5/2/2014 1:15 PM, James W. MacDonald wrote: > Hi Sean, > > This all works on Linux, and obviously on MacOS for you, but on > Windows 7, not so much: > > > gpl <- getGEO("GPL90") > File stored at: > C:\Users\BIOINF~1\AppData\Local\Temp\Rtmp4UPr1i/GPL90.soft > Warning message: > In download.file(myurl, destfile, mode = mode, quiet = TRUE, method = > getOption("download.file.method.GEOquery")) : > downloaded length 9476281 != reported length 200 > > But the gpl object looks OK, so I guess the reported length is wrong. > > > geoq <- getGEO("GSE9514", GSEMatrix = FALSE) > File stored at: > C:\Users\BIOINF~1\AppData\Local\Temp\Rtmp4UPr1i/GSE9514.soft.gz > Parsing.... > Found 9 entities... > GPL90 (1 of 9 entities) > GSM241146 (2 of 9 entities) > GSM241147 (3 of 9 entities) > GSM241148 (4 of 9 entities) > GSM241149 (5 of 9 entities) > GSM241150 (6 of 9 entities) > GSM241151 (7 of 9 entities) > GSM241152 (8 of 9 entities) > GSM241153 (9 of 9 entities) > There were 50 or more warnings (use warnings() to see the first 50) > > > geoq <- getGEO("GSE9514") > ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9514/matrix/ > Error in function (type, msg, asError = TRUE) : couldn't connect to host > > > setInternet2(use=FALSE) > > geoq <- getGEO("GSE9514") > ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9514/matrix/ > Error in function (type, msg, asError = TRUE) : > Server denied you to change to the given directory > > Any suggestions? I can't find anything on the list archives that > helps. I am thinking it has something to do with Windows Firewall, as > I can get to > > http://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9514/matrix/ > > using a browser, but not > > ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9514/matrix/ > > but setting up a specific rule under Windows Firewall to allow R.exe > ftp access doesn't seem to help. > > Best, > > Jim > > > > > On 5/2/2014 12:20 PM, Sean Davis wrote: >> Hi, again, James. >> >> NCBI is still checking into the issue (may have been a storm- related >> issue), but your (simplified) example now works for me. >> >>> gpl = getGEO('GPL90') >> File stored at: >> /var/folders/21/8t47kwys6vqb8606kdfn71780000gn/T//RtmpQXZfrr/GPL90. soft >>> sessionInfo() >> R version 3.0.2 Patched (2014-01-22 r64855) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] GEOquery_2.28.0 Biobase_2.21.7 BiocGenerics_0.7.5 >> [4] BiocInstaller_1.12.0 >> >> loaded via a namespace (and not attached): >> [1] RCurl_1.95-4.1 XML_3.95-0.2 >> >> >> Sean >> >> On Thu, May 1, 2014 at 1:11 PM, Sean Davis <sdavis2 at="" mail.nih.gov=""> wrote: >>> Hi, James. >>> >>> Thanks for the report. This is due to a change at NCBI. I am >>> checking with them to see if the change is meant to be permanent or is >>> simply a transient issue. I'll let everyone know as soon as I hear >>> back from NCBI. >>> >>> Sean >>> >>> >>> On Thu, May 1, 2014 at 9:19 AM, James W. MacDonald <jmacdon at="" uw.edu=""> >>> wrote: >>>> Hi Sean, >>>> >>>>> geoq <- getGEO("GSE9514") >>>> ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE9nnn/GSE9514/matrix/ >>>> Found 1 file(s) >>>> GSE9514_series_matrix.txt.gz >>>> % Total % Received % Xferd Average Speed Time Time Time >>>> Current >>>> Dload Upload Total Spent Left >>>> Speed >>>> 100 378k 100 378k 0 0 204k 0 0:00:01 0:00:01 >>>> --:--:-- >>>> 204k >>>> File stored at: >>>> /data3/tmp/RtmpkDXZzR/GPL90.soft >>>> Error in xj[i] : only 0's may be mixed with negative subscripts >>>> >>>> And the error appears to come from this section in parseGPL(): >>>> >>>> if (hasDataTable) { >>>> nLinesToRead <- NULL >>>> if (!is.null(n)) { >>>> nLinesToRead <- n - length(txt) >>>> } >>>> dat3 <- fastTabRead(con, n = nLinesToRead, quote = "") >>>> geoDataTable <- new("GEODataTable", columns = cols, table = >>>> dat3[1:(nrow(dat3) - >>>> 1), ]) >>>> } >>>> >>>> Where there is no error trapping for the case that fastTabRead >>>> returns a >>>> zero row data.frame: >>>> >>>> debug: dat3 <- fastTabRead(con, n = nLinesToRead, quote = "") >>>> Browse[3]> dim(dat3) >>>> [1] 0 17 >>>> Browse[3]> dat3 >>>> [1] ID ORF >>>> [3] SPOT_ID Species Scientific Name >>>> [5] Annotation Date Sequence Type >>>> [7] Sequence Source Target Description >>>> [9] Representative Public ID Gene Title >>>> [11] Gene Symbol ENTREZ_GENE_ID >>>> [13] RefSeq Transcript ID SGD accession number >>>> [15] Gene Ontology Biological Process Gene Ontology Cellular Component >>>> [17] Gene Ontology Molecular Function >>>> <0 rows> (or 0-length row.names) >>>> >>>> Best, >>>> >>>> Jim >>>> >>>> -- >>>> James W. MacDonald, M.S. >>>> Biostatistician >>>> University of Washington >>>> Environmental and Occupational Health Sciences >>>> 4225 Roosevelt Way NE, # 100 >>>> Seattle WA 98105-6099 >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor > -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099