Re: [R] Efficient way of loading files in R
Martin,
I forgot to mention.
The same command works fine when I try,gseEset2 <- getGEO('GSE76896') ,
without saving the file to a destination folder .
Output:
Found 1 file(s)
GSE76896_series_matrix.txt.gz
trying URL '
https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76896/matrix/GSE76896_series_matrix.txt.gz
'
Content type 'application/x-gzip' length 40561936 bytes (38.7 MB)
==
downloaded 38.7 MB
Parsed with column specification:
cols(
.default = col_double(),
ID_REF = col_character()
)
See spec(...) for full column specifications.
|=| 100%
84 MB
File stored at:
/tmp/RtmprygqGb/GPL570.soft
|=| 100%
80 MB
|=| 100%
75 MB
The problem occurs when I fetch the file from destination folder using
gseEset2 <- getGEO('GSE76896', destdir = "/data/")[[1]]
Found 1 file(s)
GSE76896_series_matrix.txt.gz
Using locally cached version: /data//GSE76896_series_matrix.txt.gz
Parsed with column specification:
cols(
.default = col_double(),
ID_REF = col_character()
)
See spec(...) for full column specifications.
|=| 100%
84 MB
Using locally cached version of GPL570 found here:
/data//GPL570.soft
^C
On Fri, Sep 7, 2018 at 4:08 PM Deepa wrote:
> I am also providing the output that I obtain for your kind reference,
>
> gseEset2 <- getGEO('GSE76896', destdir = "data/")[[1]]
> Found 1 file(s)
> GSE76896_series_matrix.txt.gz
> Using locally cached version: /data//GSE76896_series_matrix.txt.gz
> Parsed with column specification:
> cols(
> .default = col_double(),
> ID_REF = col_character()
> )
> See spec(...) for full column specifications.
> Using locally cached version of GPL570 found here:
> /data//GPL570.soft
>
> After this I don't see any output. I had to forcefully stop the execution.
>
> On Fri, Sep 7, 2018 at 4:05 PM Deepa wrote:
>
>> I already posted a similar issue on bioconductor.
>> https://support.bioconductor.org/p/112607/#112634
>> Couldn't find a solution.
>>
>>
>> On Fri, Sep 7, 2018 at 3:45 PM Martin Morgan
>> wrote:
>>
>>> Ask on the Bioconductor support site https://support.bioconductor.org
>>>
>>> Provide (on the support site) the output of the R commands
>>>
>>>library(GEOquery)
>>>sessionInfo()
>>>
>>> Also include (copy and paste) the output of the command that fails. I
>>> have
>>>
>>> > gseEset2 <- getGEO('GSE76896')[[1]]
>>> Found 1 file(s)
>>> GSE76896_series_matrix.txt.gz
>>> trying URL
>>> '
>>> https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76896/matrix/GSE76896_series_matrix.txt.gz
>>> '
>>> Content type 'application/x-gzip' length 40561936 bytes (38.7 MB)
>>> ==
>>> downloaded 38.7 MB
>>>
>>> Parsed with column specification:
>>> cols(
>>>.default = col_double(),
>>>ID_REF = col_character()
>>> )
>>> See spec(...) for full column specifications.
>>> |=| 100%
>>>84 MB
>>> File stored at:
>>> /tmp/Rtmpe4NWji/GPL570.soft
>>> |=| 100%
>>>75 MB
>>> > sessionInfo()
>>> R version 3.5.1 Patched (2018-08-22 r75177)
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>> Running under: Ubuntu 16.04.5 LTS
>>>
>>> Matrix products: default
>>> BLAS: /home/mtmorgan/bin/R-3-5-branch/lib/libRblas.so
>>> LAPACK: /home/mtmorgan/bin/R-3-5-branch/lib/libRlapack.so
>>>
>>> locale:
>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>>> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>
>>> attached base packages:
>>> [1] parallel stats graphics grDevices utils datasets methods
>>> [8] base
>>>
>>> other attached packages:
>>> [1] bindrcpp_0.2.2 GEOquery_2.49.1 Biobase_2.41.2
>>> [4] BiocGenerics_0.27.1 BiocManager_1.30.2
>>>
>>> loaded via a namespace (and not attached):
>>> [1] Rcpp_0.12.18 tidyr_0.8.1 crayon_1.3.4 dplyr_0.7.6
>>> [5] assertthat_0.2.0 R6_2.2.2 magrittr_1.5 pillar_1.3.0
>>> [9] stringi_1.2.4rlang_0.2.2 curl_3.2 limma_3.37.4
>>> [13] xml2_1.2.0 tools_3.5.1 readr_1.1.1 glue_1.3.0
>>> [17] purrr_0.2.5 hms_0.4.2compiler_3.5.1 pkgconfig_2.0.2
>>> [21] tidyselect_0.2.4 bindr_0.1.1 tibble_1.4.2
>>>
>>> On 09/07/2018 06:08 AM, Deepa wrote:
>>> > Hello,
>>> >
>>> > I am using a bioconductor package in R.
>>> > The command that I use reads the contents of a file downloaded from a
>>> > database and creates an expression object.
>>> >
>>> > The syntax works perfectly
Re: [R] Efficient way of loading files in R
I am also providing the output that I obtain for your kind reference,
gseEset2 <- getGEO('GSE76896', destdir = "data/")[[1]]
Found 1 file(s)
GSE76896_series_matrix.txt.gz
Using locally cached version: /data//GSE76896_series_matrix.txt.gz
Parsed with column specification:
cols(
.default = col_double(),
ID_REF = col_character()
)
See spec(...) for full column specifications.
Using locally cached version of GPL570 found here:
/data//GPL570.soft
After this I don't see any output. I had to forcefully stop the execution.
On Fri, Sep 7, 2018 at 4:05 PM Deepa wrote:
> I already posted a similar issue on bioconductor.
> https://support.bioconductor.org/p/112607/#112634
> Couldn't find a solution.
>
>
> On Fri, Sep 7, 2018 at 3:45 PM Martin Morgan
> wrote:
>
>> Ask on the Bioconductor support site https://support.bioconductor.org
>>
>> Provide (on the support site) the output of the R commands
>>
>>library(GEOquery)
>>sessionInfo()
>>
>> Also include (copy and paste) the output of the command that fails. I have
>>
>> > gseEset2 <- getGEO('GSE76896')[[1]]
>> Found 1 file(s)
>> GSE76896_series_matrix.txt.gz
>> trying URL
>> '
>> https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76896/matrix/GSE76896_series_matrix.txt.gz
>> '
>> Content type 'application/x-gzip' length 40561936 bytes (38.7 MB)
>> ==
>> downloaded 38.7 MB
>>
>> Parsed with column specification:
>> cols(
>>.default = col_double(),
>>ID_REF = col_character()
>> )
>> See spec(...) for full column specifications.
>> |=| 100%
>>84 MB
>> File stored at:
>> /tmp/Rtmpe4NWji/GPL570.soft
>> |=| 100%
>>75 MB
>> > sessionInfo()
>> R version 3.5.1 Patched (2018-08-22 r75177)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.5 LTS
>>
>> Matrix products: default
>> BLAS: /home/mtmorgan/bin/R-3-5-branch/lib/libRblas.so
>> LAPACK: /home/mtmorgan/bin/R-3-5-branch/lib/libRlapack.so
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] parallel stats graphics grDevices utils datasets methods
>> [8] base
>>
>> other attached packages:
>> [1] bindrcpp_0.2.2 GEOquery_2.49.1 Biobase_2.41.2
>> [4] BiocGenerics_0.27.1 BiocManager_1.30.2
>>
>> loaded via a namespace (and not attached):
>> [1] Rcpp_0.12.18 tidyr_0.8.1 crayon_1.3.4 dplyr_0.7.6
>> [5] assertthat_0.2.0 R6_2.2.2 magrittr_1.5 pillar_1.3.0
>> [9] stringi_1.2.4rlang_0.2.2 curl_3.2 limma_3.37.4
>> [13] xml2_1.2.0 tools_3.5.1 readr_1.1.1 glue_1.3.0
>> [17] purrr_0.2.5 hms_0.4.2compiler_3.5.1 pkgconfig_2.0.2
>> [21] tidyselect_0.2.4 bindr_0.1.1 tibble_1.4.2
>>
>> On 09/07/2018 06:08 AM, Deepa wrote:
>> > Hello,
>> >
>> > I am using a bioconductor package in R.
>> > The command that I use reads the contents of a file downloaded from a
>> > database and creates an expression object.
>> >
>> > The syntax works perfectly fine when the input size is of 10 MB.
>> Whereas,
>> > when the file size is around 40MB the object isn't created.
>> >
>> > Is there an efficient way of loading a large input file to create the
>> > expression object?
>> >
>> > This is my code,
>> >
>> >
>> > library(gcrma)
>> > library(limma)
>> > library(biomaRt)
>> > library(GEOquery)
>> > library(Biobase)
>> > require(GEOquery)
>> > require(Biobase)
>> > gseEset1 <- getGEO('GSE53454')[[1]] #filesize 10MB
>> > gseEset2 <- getGEO('GSE76896')[[1]] #file size 40MB
>> >
>> > ##gseEset2 doesn't load and isn't created
>> >
>> > Many thanks
>> >
>> > [[alternative HTML version deleted]]
>> >
>> > __
>> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> > https://stat.ethz.ch/mailman/listinfo/r-help
>> > PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> > and provide commented, minimal, self-contained, reproducible code.
>> >
>>
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficient way of loading files in R
I already posted a similar issue on bioconductor.
https://support.bioconductor.org/p/112607/#112634
Couldn't find a solution.
On Fri, Sep 7, 2018 at 3:45 PM Martin Morgan
wrote:
> Ask on the Bioconductor support site https://support.bioconductor.org
>
> Provide (on the support site) the output of the R commands
>
>library(GEOquery)
>sessionInfo()
>
> Also include (copy and paste) the output of the command that fails. I have
>
> > gseEset2 <- getGEO('GSE76896')[[1]]
> Found 1 file(s)
> GSE76896_series_matrix.txt.gz
> trying URL
> '
> https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76896/matrix/GSE76896_series_matrix.txt.gz
> '
> Content type 'application/x-gzip' length 40561936 bytes (38.7 MB)
> ==
> downloaded 38.7 MB
>
> Parsed with column specification:
> cols(
>.default = col_double(),
>ID_REF = col_character()
> )
> See spec(...) for full column specifications.
> |=| 100%
>84 MB
> File stored at:
> /tmp/Rtmpe4NWji/GPL570.soft
> |=| 100%
>75 MB
> > sessionInfo()
> R version 3.5.1 Patched (2018-08-22 r75177)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.5 LTS
>
> Matrix products: default
> BLAS: /home/mtmorgan/bin/R-3-5-branch/lib/libRblas.so
> LAPACK: /home/mtmorgan/bin/R-3-5-branch/lib/libRlapack.so
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel stats graphics grDevices utils datasets methods
> [8] base
>
> other attached packages:
> [1] bindrcpp_0.2.2 GEOquery_2.49.1 Biobase_2.41.2
> [4] BiocGenerics_0.27.1 BiocManager_1.30.2
>
> loaded via a namespace (and not attached):
> [1] Rcpp_0.12.18 tidyr_0.8.1 crayon_1.3.4 dplyr_0.7.6
> [5] assertthat_0.2.0 R6_2.2.2 magrittr_1.5 pillar_1.3.0
> [9] stringi_1.2.4rlang_0.2.2 curl_3.2 limma_3.37.4
> [13] xml2_1.2.0 tools_3.5.1 readr_1.1.1 glue_1.3.0
> [17] purrr_0.2.5 hms_0.4.2compiler_3.5.1 pkgconfig_2.0.2
> [21] tidyselect_0.2.4 bindr_0.1.1 tibble_1.4.2
>
> On 09/07/2018 06:08 AM, Deepa wrote:
> > Hello,
> >
> > I am using a bioconductor package in R.
> > The command that I use reads the contents of a file downloaded from a
> > database and creates an expression object.
> >
> > The syntax works perfectly fine when the input size is of 10 MB. Whereas,
> > when the file size is around 40MB the object isn't created.
> >
> > Is there an efficient way of loading a large input file to create the
> > expression object?
> >
> > This is my code,
> >
> >
> > library(gcrma)
> > library(limma)
> > library(biomaRt)
> > library(GEOquery)
> > library(Biobase)
> > require(GEOquery)
> > require(Biobase)
> > gseEset1 <- getGEO('GSE53454')[[1]] #filesize 10MB
> > gseEset2 <- getGEO('GSE76896')[[1]] #file size 40MB
> >
> > ##gseEset2 doesn't load and isn't created
> >
> > Many thanks
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficient way of loading files in R
Ask on the Bioconductor support site https://support.bioconductor.org
Provide (on the support site) the output of the R commands
library(GEOquery)
sessionInfo()
Also include (copy and paste) the output of the command that fails. I have
> gseEset2 <- getGEO('GSE76896')[[1]]
Found 1 file(s)
GSE76896_series_matrix.txt.gz
trying URL
'https://ftp.ncbi.nlm.nih.gov/geo/series/GSE76nnn/GSE76896/matrix/GSE76896_series_matrix.txt.gz'
Content type 'application/x-gzip' length 40561936 bytes (38.7 MB)
==
downloaded 38.7 MB
Parsed with column specification:
cols(
.default = col_double(),
ID_REF = col_character()
)
See spec(...) for full column specifications.
|=| 100%
84 MB
File stored at:
/tmp/Rtmpe4NWji/GPL570.soft
|=| 100%
75 MB
> sessionInfo()
R version 3.5.1 Patched (2018-08-22 r75177)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS
Matrix products: default
BLAS: /home/mtmorgan/bin/R-3-5-branch/lib/libRblas.so
LAPACK: /home/mtmorgan/bin/R-3-5-branch/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] bindrcpp_0.2.2 GEOquery_2.49.1 Biobase_2.41.2
[4] BiocGenerics_0.27.1 BiocManager_1.30.2
loaded via a namespace (and not attached):
[1] Rcpp_0.12.18 tidyr_0.8.1 crayon_1.3.4 dplyr_0.7.6
[5] assertthat_0.2.0 R6_2.2.2 magrittr_1.5 pillar_1.3.0
[9] stringi_1.2.4rlang_0.2.2 curl_3.2 limma_3.37.4
[13] xml2_1.2.0 tools_3.5.1 readr_1.1.1 glue_1.3.0
[17] purrr_0.2.5 hms_0.4.2compiler_3.5.1 pkgconfig_2.0.2
[21] tidyselect_0.2.4 bindr_0.1.1 tibble_1.4.2
On 09/07/2018 06:08 AM, Deepa wrote:
Hello,
I am using a bioconductor package in R.
The command that I use reads the contents of a file downloaded from a
database and creates an expression object.
The syntax works perfectly fine when the input size is of 10 MB. Whereas,
when the file size is around 40MB the object isn't created.
Is there an efficient way of loading a large input file to create the
expression object?
This is my code,
library(gcrma)
library(limma)
library(biomaRt)
library(GEOquery)
library(Biobase)
require(GEOquery)
require(Biobase)
gseEset1 <- getGEO('GSE53454')[[1]] #filesize 10MB
gseEset2 <- getGEO('GSE76896')[[1]] #file size 40MB
##gseEset2 doesn't load and isn't created
Many thanks
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficient way of loading files in R
getgeo() seems to be a custom routine. Import the file in reader and
confirm that's a CSV file from Excel. If this is a non standard input,
custom subroutine is creating new constraints. Usually R has no problem
till workspace is 1 gb
On Fri 7 Sep, 2018, 15:38 Deepa, wrote:
> Hello,
>
> I am using a bioconductor package in R.
> The command that I use reads the contents of a file downloaded from a
> database and creates an expression object.
>
> The syntax works perfectly fine when the input size is of 10 MB. Whereas,
> when the file size is around 40MB the object isn't created.
>
> Is there an efficient way of loading a large input file to create the
> expression object?
>
> This is my code,
>
>
> library(gcrma)
> library(limma)
> library(biomaRt)
> library(GEOquery)
> library(Biobase)
> require(GEOquery)
> require(Biobase)
> gseEset1 <- getGEO('GSE53454')[[1]] #filesize 10MB
> gseEset2 <- getGEO('GSE76896')[[1]] #file size 40MB
>
> ##gseEset2 doesn't load and isn't created
>
> Many thanks
>
> [[alternative HTML version deleted]]
>
> __
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
--
__
Amit Mittal
Pursuing Ph.D. in Finance and Accounting
Indian Institute of Management, Lucknow
Visit my SSRN author page:
http://ssrn.com/author=2665511
* Top 10% Downloaded Author on SSRN
Mob: +91 7525023664
This message has been sent from a mobile device. I may contact you again.
_
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Efficient way of loading files in R
The following is the system configuration:
Architecture: x86_64
CPU op-mode(s):32-bit, 64-bit
Byte Order:Little Endian
CPU(s):4
On-line CPU(s) list: 0-3
Thread(s) per core:2
Core(s) per socket:2
Socket(s): 1
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family:6
Model: 142
Model name:Intel(R) Core(TM) i7-7500U CPU @ 2.70GHz
Stepping: 9
CPU MHz: 2844.008
CPU max MHz: 3500.
CPU min MHz: 400.
BogoMIPS: 5808.00
Virtualization:VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 4096K
NUMA node0 CPU(s): 0-3
On Fri, Sep 7, 2018 at 3:38 PM Deepa wrote:
> Hello,
>
> I am using a bioconductor package in R.
> The command that I use reads the contents of a file downloaded from a
> database and creates an expression object.
>
> The syntax works perfectly fine when the input size is of 10 MB. Whereas,
> when the file size is around 40MB the object isn't created.
>
> Is there an efficient way of loading a large input file to create the
> expression object?
>
> This is my code,
>
>
> library(gcrma)
> library(limma)
> library(biomaRt)
> library(GEOquery)
> library(Biobase)
> require(GEOquery)
> require(Biobase)
> gseEset1 <- getGEO('GSE53454')[[1]] #filesize 10MB
> gseEset2 <- getGEO('GSE76896')[[1]] #file size 40MB
>
> ##gseEset2 doesn't load and isn't created
>
> Many thanks
>
>
>
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
[R] Efficient way of loading files in R
Hello,
I am using a bioconductor package in R.
The command that I use reads the contents of a file downloaded from a
database and creates an expression object.
The syntax works perfectly fine when the input size is of 10 MB. Whereas,
when the file size is around 40MB the object isn't created.
Is there an efficient way of loading a large input file to create the
expression object?
This is my code,
library(gcrma)
library(limma)
library(biomaRt)
library(GEOquery)
library(Biobase)
require(GEOquery)
require(Biobase)
gseEset1 <- getGEO('GSE53454')[[1]] #filesize 10MB
gseEset2 <- getGEO('GSE76896')[[1]] #file size 40MB
##gseEset2 doesn't load and isn't created
Many thanks
[[alternative HTML version deleted]]
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
