On Thu, Feb 24, 2011 at 7:41 AM, Ivan Gregoretti <ivangreg@gmail.com> wrote:

> Hi Michael and Janet,
>
> I think that the reduce bug still persists in the devel branch. I
> updated all my Bioconductor packages yesterday and yet, following her
> steps I get

> reduce(myregions_RD)
> Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism
>
> I hope the sessionInfo() helps.
>
>

Think this needs 1.9.25. Should be out tomorrow.

Thanks,
Michael



> Thank you,
>
> Ivan
>
> > sessionInfo()
> R version 2.13.0 Under development (unstable) (2010-12-02 r53747)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>  [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=en_US.utf8
>  [7] LC_PAPER=en_US.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] ChIPpeakAnno_1.7.0                  limma_3.7.23
>  [3] org.Hs.eg.db_2.4.6                  GO.db_2.4.5
>  [5] RSQLite_0.9-4                       DBI_0.2-5
>  [7] AnnotationDbi_1.13.13
> BSgenome.Ecoli.NCBI.20080805_1.3.17
>  [9] multtest_2.7.1                      Biobase_2.11.8
> [11] biomaRt_2.7.1                       BSgenome.Mmusculus.UCSC.mm9_1.3.17
> [13] BSgenome_1.19.3                     Biostrings_2.19.9
> [15] GenomicRanges_1.3.18                IRanges_1.9.22
>
> loaded via a namespace (and not attached):
> [1] MASS_7.3-11     RCurl_1.5-0     splines_2.13.0  survival_2.36-5
> [5] XML_3.2-0
>
>
> Ivan Gregoretti, PhD
> National Institute of Diabetes and Digestive and Kidney Diseases
> National Institutes of Health
> 5 Memorial Dr, Building 5, Room 205.
> Bethesda, MD 20892. USA.
> Phone: 1-301-496-1016 and 1-301-496-1592
> Fax: 1-301-496-9878
>
>
>
> On Thu, Feb 24, 2011 at 9:46 AM, Michael Lawrence
> <lawrence.michael@gene.com> wrote:
> > Thanks. Seems to be fixed already in devel.
> >
> > On Wed, Feb 23, 2011 at 12:15 PM, Janet Young <jayoung@fhcrc.org> wrote:
> >
> >> Hi again,
> >>
> >> I noticed that "reduce" gives an error on RangedData objects if there
> are
> >> space names that contain no ranges:
> >>        Error in endoapply(x[, by], FUN) : 'FUN' did not produce an
> >> endomorphism
> >>
> >> I can work around it, but it'd great not to need to do that.  All the
> >> details are below.
> >>
> >> thanks very much,
> >>
> >> Janet
> >>
> >> -------------------------------------------------------------------
> >>
> >> Dr. Janet Young (Trask lab)
> >>
> >> Fred Hutchinson Cancer Research Center
> >> 1100 Fairview Avenue N., C3-168,
> >> P.O. Box 19024, Seattle, WA 98109-1024, USA.
> >>
> >> tel: (206) 667 1471 fax: (206) 667 6524
> >> email: jayoung  ...at...  fhcrc.org
> >>
> >> http://www.fhcrc.org/labs/trask/
> >>
> >> -------------------------------------------------------------------
> >>
> >>
> >>
> >> > library(IRanges,warn.conflicts=F)
> >>
> >> > myregions_RD <-
> >>
> RangedData(IRanges(start=c(101L,201L,101L,101L),end=c(250L,300L,220L,501L)),space=c("chr1","chr1","chr1","chr2"),strand=c("+","+","+","+")
> >>   )
> >>
> >> > #### this works
> >> > reduce(myregions_RD)
> >> RangedData with 2 rows and 1 value column across 2 spaces
> >>        space     ranges |      strand
> >>  <character>  <IRanges> | <character>
> >> 1        chr1 [101, 300] |           +
> >> 2        chr2 [101, 501] |           +
> >>
> >> > ### drop regions that are bigger than 300bp (now there's nothing left
> on
> >> chr2)
> >> > myregions_RD <- myregions_RD[which(width(myregions_RD)<=300),]
> >>
> >> > ### this doesn't work - reduce doesn't like a space without any
> elements
> >> > reduce(myregions_RD)
> >> Error in endoapply(x[, by], FUN) : 'FUN' did not produce an endomorphism
> >>
> >> > ### workaround - drop the unused space names
> >> > myregions_RD <-
> >>
> RangedData(IRanges(start=start(myregions_RD),end=end(myregions_RD)),space=as.character(space(myregions_RD)),strand=myregions_RD$strand
> >>   )
> >>
> >> > ### now it works
> >> > reduce(myregions_RD)
> >> RangedData with 1 row and 1 value column across 1 space
> >>        space     ranges |      strand
> >>  <character>  <IRanges> | <character>
> >> 1        chr1 [101, 300] |           +
> >>
> >> > sessionInfo()
> >> R version 2.12.1 (2010-12-16)
> >> Platform: i386-apple-darwin9.8.0/i386 (32-bit)
> >>
> >> locale:
> >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> >>
> >> attached base packages:
> >> [1] stats     graphics  grDevices utils     datasets  methods   base
> >>
> >> other attached packages:
> >> [1] IRanges_1.8.9
> >>
> >> _______________________________________________
> >> Bioc-sig-sequencing mailing list
> >> Bioc-sig-sequencing@r-project.org
> >> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> >>
> >
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> >
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