[BioC] GEOquery problem
David martin
vilanew at gmail.com
Mon Jun 14 14:20:41 CEST 2010
Sean,
Here is the complete script.
> 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="/home/dvi/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 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] GEOquery_2.13.2 RCurl_1.4-2 bitops_1.0-4.1 Biobase_2.8.0
On 06/14/2010 12:52 PM, Sean Davis wrote:
> On Mon, Jun 14, 2010 at 3:46 AM, David martin<vilanew at 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 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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