Heyi,

I'm glad you were able to generate the report using the .rda file.

We don't have any plans to support type=pdf for the qa report in the
future. The better long term solution would be to recompile R with jpeg
enabled (appropriate library installed) on the remote machine where you
are working. If jpeg is enabled you will be able to generate the html
report. See the R Installation and Administration manual at
http://www.r-project.org/.


Take care,
Valerie




On 10/07/2010 12:12 PM, heyi xiao wrote:
>
> Hi Valerie,
>
> Sorry to get back to you late, as I haven’t really got time to work on
> the problem till now.
>
> Yes, it works when I save the qa object as a .rda file and generate
> the report on my local machine with jpeg support. However, I am still
> curious why can’t we just generate PDF instead of html report? Will
> you work on the PDF report format in the future? That could make
> things easier for all machines/users. Thanks!
>
> Heyi
>
>
>
> --- On *Sun, 9/26/10, Valerie Obenchain /<vobencha@fhcrc.org>/* wrote:
>
>
>     From: Valerie Obenchain <vobencha@fhcrc.org>
>     Subject: Re: ShortRead for sequencing data quality assessment
>     To: "heyi xiao" <xiaoheyiyh@yahoo.com>
>     Cc: bioconductor@stat.math.ethz.ch
>     Date: Sunday, September 26, 2010, 5:40 PM
>
>     On 09/25/2010 08:22 AM, heyi xiao wrote:
>>     Thanks Valerie,
>>     Now I understand the readQualityScore. I ran your example code,
>>     the first few steps worked well till the report generation step.
>>     I got the same error as in my own example.
>>
>>     > report(res)
>>     Error in X11(paste("jpeg::", quality, ":", filename, sep = ""),
>>     width,  :
>>       unable to start device JPEG
>>     In addition: Warning message:
>>     In jpeg(file.path(imgDir, jpegFile), ...) :
>>       no jpeg support in this version of R
>>
>>     It seems to me that I will have to ungrade to R 2.12. If I
>>     ungrade, the bioconductor I get will be the devel version using
>>     biocLite(), right?
>>
>>     Below is my current session info. Thanks again for the help!
>>
>     Yes, if you install R 2.12 and biocLite("ShortRead") you will get
>     the most recent devel version of ShortRead.
>     However, your problem appears to be with report generation only
>     and not creating the qa() object so
>     using the devel version will not help us here. I previously
>     thought you were having problems
>     generating a qa() object which is why I provided the example code.
>     Sorry for the misunderstanding.
>
>     The report generation requires jpeg capabilities and you don't
>     appear to have this on the
>     remote machine that you are running on. I think the quickest fix
>     would be to save
>     the qa() object as an .rda file then move this file to your local
>     R machine. (This .rda file
>     is small even if your data are large.) You can then load() the
>     .rda into an R session on
>     your local machine and generate the report there. It is much more
>     likely that you
>     will have jpeg support on your local machine.
>
>     I sent an email yesterday (9/25) where I mention another option of
>     recompiling R
>     with jpeg support enabled.
>
>     Hopefully the .rda file option works for you. Let me know how it goes.
>
>     Valerie
>
>
>
>
>>
>>     > sessionInfo()
>>     R version 2.11.1 (2010-05-31)
>>     x86_64-unknown-linux-gnu
>>
>>     locale:
>>      [1] LC_CTYPE=en_US       LC_NUMERIC=C         LC_TIME=en_US      
>>      [4] LC_COLLATE=en_US     LC_MONETARY=C        LC_MESSAGES=en_US  
>>      [7] LC_PAPER=en_US       LC_NAME=C            LC_ADDRESS=C       
>>     [10] LC_TELEPHONE=C       LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
>>
>>     attached base packages:
>>     [1] stats     graphics  grDevices utils     datasets  methods  
>>     base    
>>
>>     other attached packages:
>>      [1] CSAMA10_0.0.3          chipseq_0.4.1         
>>     GenomicFeatures_1.0.10
>>      [4] biomaRt_2.4.0          BSgenome_1.16.5       
>>     EatonEtAlChIPseq_0.0.1
>>      [7] rtracklayer_1.8.1      RCurl_1.4-3           
>>     bitops_1.0-4.1       
>>     [10] ShortRead_1.6.2        Rsamtools_1.0.8       
>>     lattice_0.18-8       
>>     [13] Biostrings_2.16.9      GenomicRanges_1.0.9   
>>     IRanges_1.6.17       
>>
>>     loaded via a namespace (and not attached):
>>     [1] Biobase_2.8.0 DBI_0.2-5     grid_2.11.1   hwriter_1.2  
>>     RSQLite_0.9-2
>>     [6] tools_2.11.1  XML_3.1-1   
>>
>>
>
>


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