That worked! download.file(myurl, destfile=myfile, mode="wb")
Thanks a lot, paolo On 01/21/2011 02:53 PM, William Dunlap wrote:
Try mode="wb" ('b' for binary mode) in the call to download.file(). It should make a difference on Windows (& Mac?) and be innocuous on Unix. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com-----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Paolo Innocenti Sent: Thursday, January 20, 2011 4:39 PM To: r-help@r-project.org Subject: [R] Reading gz compressed csv file - 'incomplete line found' Hi all, I am trying to download, decompress and read a csv file. My code: myurl<- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE2 4729/GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # myfile<- "GSE24729_MitoNuclear_suppl_male_stats.csv.gz" # download.file(myurl, destfile=myfile, mode="w") # mycon<- gzcon(gzfile(myfile, open="r")) # mydata<- read.csv(textConnection(readLines(mycon))) # close(mycon) works under my linux distribution, but under windows, I get the following warning: > myurl<- "ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE2 4729/GSE24729_MitoNuclear_suppl_male_stats.csv.gz" > myfile<- "GSE24729_MitoNuclear_suppl_male_stats.csv.gz" > download.file(myurl, destfile=myfile, mode="w") trying URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE2 4729/GSE24729_MitoNuclear_suppl_male_stats.csv.gz' ftp data connection made, file length 535641 bytes opened URL downloaded 523 Kb > mycon<- gzcon(gzfile(myfile, open="r")) > mydata<- read.csv(textConnection(readLines(mycon))) Warning message: In readLines(mycon) : incomplete final line found on 'gzcon(GSE24729_MitoNuclear_suppl_male_stats.csv.gz)' > close(mycon) I can read only 30 lines, and then stops working. Does anyone have any suggestion? I suspect the problem lies in gzcon/gzfile not decompressing properly, or in some other problem with the end of line/end of file, but the help files are a bit above my level of understanding. Thanks, paolo > sessionInfo() R version 2.12.1 (2010-12-16) Platform: i386-pc-mingw32/i386 (32-bit) locale: [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] grid stats graphics grDevices utils datasets methods [8] base other attached packages: [1] lattice_0.19-13 drosophila2.db_2.4.5 org.Dm.eg.db_2.4.6 [4] GOstats_2.16.0 RSQLite_0.9-4 DBI_0.2-5 [7] graph_1.28.0 Category_2.16.0 AnnotationDbi_1.12.0 [10] xtable_1.5-6 GEOquery_2.16.3 ellipse_0.3-5 [13] RColorBrewer_1.0-2 hopach_2.10.0 cluster_1.13.2 [16] limma_3.6.9 genefilter_1.32.0 vsn_3.18.0 [19] affy_1.28.0 Biobase_2.10.0 loaded via a namespace (and not attached): [1] affyio_1.18.0 annotate_1.28.0 GO.db_2.4.5 [4] GSEABase_1.12.2 preprocessCore_1.12.0 RBGL_1.26.0 [7] RCurl_1.5-0.1 splines_2.12.1 survival_2.36-2 [10] tools_2.12.1 XML_3.2-0.2 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
