On Mon, Jun 14, 2010 at 3:46 AM, David martin <vilanew@gmail.com> wrote:

> Sean,
> I have upgraded to GEOquery  2.13.2 but the problem is still there ?? which
> version fixes that issue ?
>
>
It is working for me.  Do you mind some sessionInfo() and the exact code you
are using?

Thanks,
Sean

> gse = getGEO("GSE21630",GSEMatrix=FALSE)
File stored at:
/var/folders/F+/F+PwkbXqF6WeunvinD8pZk+++TI/-Tmp-//Rtmp1gPqTg/GSE21630.soft
Parsing....
Found 47 entities...
GPL9250 (1 of 47 entities)
GSM539835 (2 of 47 entities)
....
GSM539879 (46 of 47 entities)
GSM539880 (47 of 47 entities)
> sessionInfo()
R version 2.12.0 Under development (unstable) (2010-04-30 r51866)
i386-apple-darwin9.8.0

locale:
[1] en_US/en_US/C/C/en_US/en_US

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

other attached packages:
[1] GEOquery_2.13.2 RCurl_1.4-2     bitops_1.0-4.1  Biobase_2.9.0

loaded via a namespace (and not attached):
[1] XML_3.1-0



> thanks
>
>
>
> On 06/10/2010 03:55 PM, Sean Davis wrote:
>
>> On Thu, Jun 10, 2010 at 9:01 AM, David martin<vilanew@gmail.com>  wrote:
>>
>>  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
>>>
>>>
>> Hi, David.
>>
>> Yep.  It's a bug.  Thanks for the report.  The change has been committed
>> to
>> the release and devel branches and should be available soon in the next
>> day
>> or so.  If you need it sooner, you can checkout from svn.
>>
>> Sean
>>
>>
>>
>>  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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>>>>>
>>>>
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