Hi Ren?, Yanju, The bug has been fixed in both release and development. It took longer as first it was a complex one, second it was around the Bioc release time and third another bug appeared in another dependencies while I was testing it. Concerning the long time to generate the geneModel, I've seen that as well and that is again a behavior that has changed between Bioc 2.10 and 2.11. I'm working on it, thanks for your patience. Cheers, Nico --------------------------------------------------------------- Nicolas Delhomme Genome Biology Computational Support European Molecular Biology Laboratory Tel: +49 6221 387 8310 Email: nicolas.delhomme at embl.de Meyerhofstrasse 1 - Postfach 10.2209 69102 Heidelberg, Germany --------------------------------------------------------------- On Sep 28, 2012, at 8:52 AM, Ren? B?ttcher wrote: > Hi Nico, > > That is correct, glad to hear that you already tracked down the bug. > > Kind regards, > Ren? > >> Hi Ren?, >> >> I suppose that's the email you mentioned would be on hold, right? >> >> Nico >> >> --------------------------------------------------------------- >> Nicolas Delhomme >> >> Genome Biology Computational Support >> >> European Molecular Biology Laboratory >> >> Tel: +49 6221 387 8310 >> Email: nicolas.delhomme at embl.de >> Meyerhofstrasse 1 - Postfach 10.2209 >> 69102 Heidelberg, Germany >> --------------------------------------------------------------- >> >> >> >> >> >> On Sep 27, 2012, at 10:51 AM, Ren?B?ttcher wrote: >> >>>> Dear Ren?, >>>> >>>> The best place to post this - where you would get for sure my attention - is >>> the bioconductor mailing list. The >>>> advantage is that other developers/users might be able to help you as your >>> message would have a better >>>> visibility to the R/Bioc community. I've actually put that mailing list in Cc. >>>> >>>> There indeed seem to be a sub-setting error somewhere within the function that >>> parses the read >>>> information, or so I guess from your error message. Would it be possible for >>> you to share your >>>> EMC_18_alignment.bam file? I can set up a folder in my dropbox for you to >>> upload the file. If that is not >>>> possible, can you at least trim your bam file to the smallest size sufficient >>> to reproduce the error and >>>> share that excerpt with me? >>>> >>>> Best, >>>> >>>> Nico >>>> >>>> --------------------------------------------------------------- >>>> Nicolas Delhomme >>>> >>>> Genome Biology Computational Support >>>> >>>> European Molecular Biology Laboratory >>>> >>>> Tel: +49 6221 387 8310 >>>> Email: nicolas.delhomme at ... >>>> Meyerhofstrasse 1 - Postfach 10.2209 >>>> 69102 Heidelberg, Germany >>>> --------------------------------------------------------------- >>>> >>>> On Sep 20, 2012, at 2:04 PM, Ren? B?ttcher wrote: >>>> >>>>> Dear Mr. Delhomme, >>>>> >>>>> I would like to ask for your support concerning a problem I'm facing when >>> using your easyRNASeq package. >>>> There seems to be an issue in one of the subfunctions, >>>>> however, I am not able to tell which one, as the error message is rather >>> short. >>>>> "Error in mk_singleBracketReplacementValue(x, value) : >>>>> 'value' must be a CompressedIntegerList object" >>>>> >>>>> Please not that I'm trying to follow the example cases you provided and I am >>> currently using the developer >>>> version since my alignments require multiple reads length support according to >>> your current stable >>>> release. You can find a detailed problem description on Seqanswers, as it >>> seems I am not the only one >>>> encountering this problem. >>>>> http://seqanswers.com/forums/showthread.php?t=23477 >>>>> >>>>> With kind regards, >>>>> Ren? B?ttcher >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at ... >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>> >>> Dear Nicolas, >>> >>> I ran picard-tools FixMateInformation on my bam-file, however, it did not solve >>> the problem. Additionally, the problem also occurs with another sample, so I >>> will now crop both of these bam-files to reduce their size and still retain >>> reproducibility. If you could provide me with your dropbox folder, I can then >>> upload them for you to test where the bug occurs. >>> >>> Thank you for your support. >>> >>> With kind regards, >>> Ren? >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >