[BioC] GEOquery problem

Mon Jun 14 09:46:04 CEST 2010

Sean,
I have upgraded to GEOquery  2.13.2 but the problem is still there ?? 
which version fixes that issue ?

thanks

On 06/10/2010 03:55 PM, Sean Davis wrote:
> On Thu, Jun 10, 2010 at 9:01 AM, David martin<vilanew at 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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