[BioC] GEOquery problem

[David martin]

Sean,
Yes you're right, that was a problem with file location but i still have 
a problem, see log file below....

A turn around for me was:

 > 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)'.

Loading required package: RCurl
Loading required package: bitops
 > data="extdata/GSE21630_family.soft.gz"
 > gse <- getGEO(filename=data,GSEMatrix=FALSE)
Parsing....
Found 47 entities...
GPL9250 (1 of 47 entities)
Error in read.table(file = file, header = header, sep = sep, quote = 
quote,  :
   no lines available in input
 > sessionInfo()
R version 2.11.0 (2010-04-22)
i686-pc-linux-gnu

locale:
  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8
  [7] LC_PAPER=ca_AD.UTF-8       LC_NAME=C
  [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=ca_AD.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] GEOquery_2.12.0 RCurl_1.4-2     bitops_1.0-4.1  Biobase_2.8.0
 >






On 06/09/2010 06:12 PM, James W. MacDonald wrote:
> Hi David,
>
> David martin wrote:
>> It looks to me that there might some problem with softfiles. Did
>> anybody came across a similar problem ??
>>
>>
>> library(GEOquery)
>> gse <- getGEO(filename =
>> system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery"))
>>
>> Error in read.table(con, sep = "\t", header = FALSE, nrows = nseries) :
>> invalid 'nlines' argument
>> In addition: Warning messages:
>> 1: In file(fname, "r") :
>> file("") only supports open = "w+" and open = "w+b": using the former
>> 2: In file(con, "r") :
>> file("") only supports open = "w+" and open = "w+b": using the former
>> 3: In file(fname, "r") :
>> file("") only supports open = "w+" and open = "w+b": using the former
>
> You have to point to a file that actually exists!
>
>  > system.file("extdata/GSE21630_family.soft.gz",package = "GEOquery")
> [1] ""
>
> If I use the softfile in that directory, it works for me.
>
>  > gse <- getGEO(filename =
> system.file("extdata/GSE781_family.soft.gz",package = "GEOquery"),
> GSEMatrix=FALSE)
> Parsing....
> Found 36 entities...
> GPL96 (1 of 36 entities)
> GPL97 (2 of 36 entities)
> GSM11805 (3 of 36 entities)
> GSM11810 (4 of 36 entities)
> GSM11814 (5 of 36 entities)
> GSM11815 (6 of 36 entities)
> GSM11823 (7 of 36 entities)
> GSM11827 (8 of 36 entities)
> GSM11830 (9 of 36 entities)
> GSM11832 (10 of 36 entities)
> GSM12067 (11 of 36 entities)
> GSM12069 (12 of 36 entities)
> GSM12075 (13 of 36 entities)
> GSM12078 (14 of 36 entities)
> GSM12079 (15 of 36 entities)
> GSM12083 (16 of 36 entities)
> GSM12098 (17 of 36 entities)
> GSM12099 (18 of 36 entities)
> GSM12100 (19 of 36 entities)
> GSM12101 (20 of 36 entities)
> GSM12105 (21 of 36 entities)
> GSM12106 (22 of 36 entities)
> GSM12268 (23 of 36 entities)
> GSM12269 (24 of 36 entities)
> GSM12270 (25 of 36 entities)
> GSM12274 (26 of 36 entities)
> GSM12283 (27 of 36 entities)
> GSM12287 (28 of 36 entities)
> GSM12298 (29 of 36 entities)
> GSM12299 (30 of 36 entities)
> GSM12300 (31 of 36 entities)
> GSM12301 (32 of 36 entities)
> GSM12399 (33 of 36 entities)
> GSM12412 (34 of 36 entities)
> GSM12444 (35 of 36 entities)
> GSM12448 (36 of 36 entities)
>
>  > sessionInfo()
> R version 2.11.0 Patched (2010-05-01 r51890)
> i386-pc-mingw32
>
> 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] stats graphics grDevices datasets utils methods base
>
> other attached packages:
> [1] GEOquery_2.12.0 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0
>
> loaded via a namespace (and not attached):
> [1] tools_2.11.0
>
> Best,
>
> Jim
>
>
>
>>
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>