Reading gz compressed csv file - 'incomplete line found'

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-bounces at r-project.org
[mailto:r-help-bounces at r-project.org] On Behalf Of Paolo Innocenti
Sent: Thursday, January 20, 2011 4:39 PM
To: r-help at 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