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   [[alternative HTML version deleted]]

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 >> >> > > [[alternative HTML version deleted]]