Hi I am trying to get GSE24080 from GEO using getGeo() function in Geoquery package and get several warnings. Can anyone please help me clear out the warnings and get successful download? I am using R version 2.13.1 (2011-07-08) on Windows XP. Thanks.--Silav > Sys.getlocale() [1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252" > library(GEOquery) Loading required package: Biobase Welcome to Bioconductor   Vignettes contain introductory material. To view, type   'browseVignettes()'. To cite Bioconductor, see   'citation("Biobase")' and for packages 'citation("pkgname")'. Setting options('download.file.method.GEOquery'='curl') Warning message: '.readRDS' is deprecated. Use 'readRDS' instead. See help("Deprecated") > gse24080 <- getGEO("GSE24080") Found 3 file(s) GSE24080_series_matrix-1.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/ GSE24080_series_matrix-1.txt.gz' ftp data connection made, file length 38807310 bytes opened URL downloaded 37.0 Mb File stored at: C:\DOCUME~1\....... GSE24080_series_matrix-2.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/ GSE24080_series_matrix-2.txt.gz' ftp data connection made, file length 38738618 bytes opened URL downloaded 36.9 Mb Using locally cached version of GPL570 found here: C:\DOCUME~1\......... GSE24080_series_matrix-3.txt.gz trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE24080/ GSE24080_series_matrix-3.txt.gz' ftp data connection made, file length 7721111 bytes opened URL downloaded 7.4 Mb Using locally cached version of GPL570 found here: C:\DOCUME~1\........ There were 15 warnings (use warnings() to see them) > warnings() Warning messages: 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :   seek on a gzfile connection returned an internal error 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :   seek on a gzfile connection returned an internal error 3: In readLines(con, 1) : seek on a gzfile connection returned an internal error 4: In read.table(file = file, header = header, sep = sep,  ... :   seek on a gzfile connection returned an internal error 5: In read.table(file = file, header = header, sep = sep,  ... :   seek on a gzfile connection returned an internal error 6: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :   seek on a gzfile connection returned an internal error 7: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :   seek on a gzfile connection returned an internal error 8: In readLines(con, 1) : seek on a gzfile connection returned an internal error 9: In read.table(file = file, header = header, sep = sep,  ... :   seek on a gzfile connection returned an internal error 10: In read.table(file = file, header = header, sep = sep,  ... :   seek on a gzfile connection returned an internal error 11: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) :   seek on a gzfile connection returned an internal error 12: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) :   seek on a gzfile connection returned an internal error 13: In readLines(con, 1) : seek on a gzfile connection returned an internal error 14: In read.table(file = file, header = header, sep = sep,  ... :   seek on a gzfile connection returned an internal error 15: In read.table(file = file, header = header, sep = sep,  ... :   seek on a gzfile connection returned an internal error > --Silav [[alternative HTML version deleted]]

On Sat, Sep 17, 2011 at 11:25 PM, Silav Bremos <silavb at="" yahoo.com=""> wrote: > Hi > I am trying to get GSE24080 from GEO using getGeo() function in Geoquery package and get several warnings. > > Can anyone please help me clear out the warnings and get successful download? I am using R version 2.13.1 (2011-07-08) > on Windows XP. Thanks.--Silav > Hi, Silav. The download worked fine and you should be able to proceed with your analyses. These are warnings, not errors. I need to clean up the warnings (which arise from some functions in base R and not in GEOquery, directly), but in the meantime, you can ignore them. Sean > >> Sys.getlocale() > [1] "LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252" > > >> library(GEOquery) > Loading required package: Biobase > Welcome to Bioconductor > ? Vignettes contain introductory material. To view, type > ? 'browseVignettes()'. To cite Bioconductor, see > ? 'citation("Biobase")' and for packages 'citation("pkgname")'. > Setting options('download.file.method.GEOquery'='curl') > Warning message: > '.readRDS' is deprecated. > Use 'readRDS' instead. > See help("Deprecated") > >> gse24080 <- getGEO("GSE24080") > Found 3 file(s) > GSE24080_series_matrix-1.txt.gz > trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2408 0/GSE24080_series_matrix-1.txt.gz' > ftp data connection made, file length 38807310 bytes > opened URL > downloaded 37.0 Mb > > File stored at: > C:\DOCUME~1\....... > GSE24080_series_matrix-2.txt.gz > trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2408 0/GSE24080_series_matrix-2.txt.gz' > ftp data connection made, file length 38738618 bytes > opened URL > downloaded 36.9 Mb > > Using locally cached version of GPL570 found here: > C:\DOCUME~1\......... > GSE24080_series_matrix-3.txt.gz > trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2408 0/GSE24080_series_matrix-3.txt.gz' > ftp data connection made, file length 7721111 bytes > opened URL > downloaded 7.4 Mb > > Using locally cached version of GPL570 found here: > C:\DOCUME~1\........ > There were 15 warnings (use warnings() to see them) >> warnings() > Warning messages: > 1: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > ? seek on a gzfile connection returned an internal error > 2: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : > ? seek on a gzfile connection returned an internal error > 3: In readLines(con, 1) : seek on a gzfile connection returned an internal error > 4: In read.table(file = file, header = header, sep = sep,? ... : > ? seek on a gzfile connection returned an internal error > 5: In read.table(file = file, header = header, sep = sep,? ... : > ? seek on a gzfile connection returned an internal error > 6: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > ? seek on a gzfile connection returned an internal error > 7: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : > ? seek on a gzfile connection returned an internal error > 8: In readLines(con, 1) : seek on a gzfile connection returned an internal error > 9: In read.table(file = file, header = header, sep = sep,? ... : > ? seek on a gzfile connection returned an internal error > 10: In read.table(file = file, header = header, sep = sep,? ... : > ? seek on a gzfile connection returned an internal error > 11: In read.table(con, sep = "\t", header = FALSE, nrows = nseries) : > ? seek on a gzfile connection returned an internal error > 12: In read.table(con, sep = "\t", header = FALSE, nrows = nsamples) : > ? seek on a gzfile connection returned an internal error > 13: In readLines(con, 1) : seek on a gzfile connection returned an internal error > 14: In read.table(file = file, header = header, sep = sep,? ... : > ? seek on a gzfile connection returned an internal error > 15: In read.table(file = file, header = header, sep = sep,? ... : > ? seek on a gzfile connection returned an internal error >> > > > --Silav > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > 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 >