but.. I have another different error with a different dataset.

k1.ranges = GRanges(
  seqnames=paste("chr",CEUstats.variants$chromosome,sep=""),
  IRanges(start=CEUstats.variants$position,
          width=1)
  )

> head(k1.ranges)
GRanges with 6 ranges and 0 elementMetadata cols:
      seqnames             ranges strand
         <Rle>          <IRanges>  <Rle>
  [1]     chr1 [1177919, 1177919]      *
  [2]     chr1 [1234763, 1234763]      *
  [3]     chr1 [1246257, 1246257]      *
  [4]     chr1 [1564953, 1564953]      *
  [5]     chr1 [1887112, 1887112]      *
  [6]     chr1 [1900107, 1900107]      *
  ---
  seqlengths:
    chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 ... chr22  chr3  chr4  chr5  chr6  chr7  chr8  chr9
      NA    NA    NA    NA    NA    NA    NA    NA    NA ...    NA    NA    NA    NA    NA    NA    NA    NA

> k1.locations = locateVariants(k1.ranges, txdb19)
Error in DataFrame(queryID = which(intergenic), location = location, txID = NA_integer_,  :
  different row counts implied by arguments

sessionInfo is the same as below.
thanks very much,

Francesco


On 11 Mar 2012, at 18:53, Lescai, Francesco wrote:

Adopted the suggestion of Steve and went the "hard" way of re-compiling from source the packages in my session.
not it seems to work :-))
therefore, no idea where the problem was but at least it is solved!
VariantAnnotation is no .63 instead of .61, that might have changed few things together with the other packages.

this is my session in case it might be useful for the developers.

thanks very much for your help!!
Francesco


sessionInfo()
R Under development (unstable) (2012-01-20 r58146)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.4 GenomicFeatures_1.7.30
[3] AnnotationDbi_1.17.27                   Biobase_2.15.4
[5] VariantAnnotation_1.1.63                Rsamtools_1.7.40
[7] Biostrings_2.23.6                       GenomicRanges_1.7.34
[9] IRanges_1.13.30                         BiocGenerics_0.1.14

loaded via a namespace (and not attached):
[1] BSgenome_1.23.4    DBI_0.2-5          Matrix_1.0-4       RCurl_1.91-1       RSQLite_0.11.1
[6] XML_3.9-4          biomaRt_2.11.1     bitops_1.0-4.1     ggplot2_0.8.9      grid_2.15.0
[11] lattice_0.20-0     plyr_1.7.1         rtracklayer_1.15.7 snpStats_1.5.5     splines_2.15.0
[16] stats4_2.15.0      survival_2.36-12   tools_2.15.0       zlibbioc_1.1.1


On 11 Mar 2012, at 18:34, Martin Morgan wrote:

On 03/11/2012 10:39 AM, Lescai, Francesco wrote:
Hi, this is the traceback output.

traceback()
12: stop(gettextf("invalid names for slots of class %s: %s", dQuote(Class),
       paste(snames[is.na(which)], collapse = ", ")), domain = NA)
11: initialize(value, ...)
10: initialize(value, ...)
9: new("RangesMatching", matchMatrix = matchMatrix, DIM = DIM)
8: .local(query, subject, maxgap, minoverlap, type, select, ...)
7: findOverlaps(query, unlistSubject, maxgap = maxgap, type = type,
      select = "all", ignore.strand = ignore.strand)
6: findOverlaps(query, unlistSubject, maxgap = maxgap, type = type,
      select = "all", ignore.strand = ignore.strand)
5: .local(query, subject, maxgap, minoverlap, type, select, ...)
4: findOverlaps(queryAdj, cdsByTx, type = "within")
3: findOverlaps(queryAdj, cdsByTx, type = "within")

'cdsByTx' isn't used in this context in VariantAnnotation 1.1.61, which has two lines like

 cdsCO <- countOverlaps(query, cache[["cdsByTx"]], type="within")
 txFO <- findOverlaps(query, cache[["tx"]], type="within")

that might be the current implementation. This line

cdsFO <- findOverlaps(queryAdj, cdsByTx, type="within")

_is_ in VariantAnnotation 1.0.5; I think you are getting the wrong version of VariantAnnotation, but this is not consistent with your sessionInfo().

Martin


2: locateVariants(my.ranges, txdb19)
1: locateVariants(my.ranges, txdb19)

I tried to install the package, but it seems it still picks up the old version.

biocLite("TxDb.Hsapiens.UCSC.hg19.knownGene")
BioC_mirror: http://bioconductor.org
Using R version 2.15, BiocInstaller version 1.3.7.
Installing package(s) 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Installing package(s) into Ś/Library/Frameworks/R.framework/Versions/2.15/Resources/library‚
(as Ślib‚ is unspecified)
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/macosx/leopard/contrib/2.15
trying URL 'http://bioconductor.org/packages/2.10/data/annotation/bin/macosx/leopard/contrib/2.15/TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2.tgz'
Content type 'application/x-gzip' length 16722765 bytes (15.9 Mb)
opened URL
==================================================
downloaded 15.9 Mb

and I checked on the website for the 2.10 release and the Mac version of the packages seems to be still 2.6.2.

Is there any other package I can try to install manually?
It seems now I cannot access to the developer wiki of BioC.

thanks
Francesco





On 10 Mar 2012, at 19:01, Martin Morgan wrote:

On 03/10/2012 10:14 AM, Lescai, Francesco wrote:
Thanks Martin,
done, but I still get the same error.

I can't spot the problem; maybe someone else will chime in.

(a) TxDb.Hsapiens... is still out-of-date; maybe it isn't checked by biocLite()

(b) the error

my.locations = locateVariants(my.ranges, txdb19)
Error in initialize(value, ...) :
  invalid names for slots of class „RangesMatching‰: matchMatrix, DIM

definitely looks like an 'old package' issue -- the RangesMatching class was replaced by the 'Hits' class during this release cycle. It might help to call

traceback()

after the error, and to confirm that you are accessing only functions defined in the loaded packages by starting your R session with

R --vanilla

Obviously, the sessionInfo() needs to reflect the session the command fails in not, e.g., R gui in one instance and the terminal in the other.

Martin


My new sessionInfo is

sessionInfo()
R Under development (unstable) (2012-01-20 r58146)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] BiocInstaller_1.3.7                     TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2
[3] GenomicFeatures_1.7.30                  VariantAnnotation_1.1.61
[5] Rsamtools_1.7.38                        Biostrings_2.23.6
[7] AnnotationDbi_1.17.27                   Biobase_2.15.4
[9] GenomicRanges_1.7.33                    IRanges_1.13.28
[11] BiocGenerics_0.1.12                     biomaRt_2.11.1

loaded via a namespace (and not attached):
[1] BSgenome_1.23.4    DBI_0.2-5          Matrix_1.0-4       RCurl_1.91-1       RSQLite_0.11.1
[6] XML_3.9-4          bitops_1.0-4.1     ggplot2_0.8.9      grid_2.15.0        lattice_0.20-0
[11] plyr_1.7.1         rtracklayer_1.15.7 snpStats_1.5.5     splines_2.15.0     survival_2.36-12
[16] tools_2.15.0       zlibbioc_1.1.1


On 10 Mar 2012, at 17:50, Martin Morgan wrote:

On 03/10/2012 09:39 AM, Lescai, Francesco wrote:
Hi there,
maybe I'm just doing a silly error somewhere, but I get an error when trying to locate the variants from a GRanges object.
I have a file with SNP positions, thefore I build up the GRanges this way

my.ranges = GRanges(
 seqnames=paste("chr", my.snp.unique$chromosome, sep=""),
 IRanges(start= my.snp.unique$position,
         width=1))

head(my.ranges)
GRanges with 6 ranges and 0 elementMetadata values:
     seqnames               ranges strand
        <Rle>               <IRanges>     <Rle>
 [1]     chr1 [ 1323144,  1323144]      *
 [2]     chr1 [ 3544236,  3544236]      *
 [3]     chr1 [ 6252966,  6252966]      *
 [4]     chr1 [ 7861154,  7861154]      *
 [5]     chr1 [10425118, 10425118]      *
 [6]     chr1 [10502308, 10502308]      *
 ---
 seqlengths:
   chr1 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 ...  chr4  chr5  chr6  chr7  chr8  chr9  chrX  chrY
     NA    NA    NA    NA    NA    NA    NA    NA    NA ...    NA    NA    NA    NA    NA    NA    NA    NA

library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb19<- TxDb.Hsapiens.UCSC.hg19.knownGene
#
my.locations = locateVariants(my.ranges, txdb19)
Error in initialize(value, ...) :
 invalid names for slots of class „RangesMatching‰: matchMatrix, DIM

What am I doing wrong?

Your devel packages are out of date, so I'd start with

source("http://bioconductor.org/biocLite.R")
biocLite(character())

Martin


thanks,
Francesco


sessionInfo()
R Under development (unstable) (2012-01-20 r58146)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.6.2 GenomicFeatures_1.6.7
[3] VariantAnnotation_1.1.33                Rsamtools_1.7.27
[5] Biostrings_2.23.6                       AnnotationDbi_1.17.15
[7] Biobase_2.15.3                          GenomicRanges_1.7.16
[9] IRanges_1.13.22                         BiocGenerics_0.1.4
[11] biomaRt_2.11.1

loaded via a namespace (and not attached):
[1] BSgenome_1.23.2    DBI_0.2-5          Matrix_1.0-3       RCurl_1.9-5        RSQLite_0.11.1
[6] XML_3.8-0          bitops_1.0-4.1     ggplot2_0.8.9      grid_2.15.0        lattice_0.20-0
[11] plyr_1.7.1         rtracklayer_1.15.7 snpStats_1.5.3     splines_2.15.0     survival_2.36-10
[16] tools_2.15.0       zlibbioc_1.1.1

---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development&    Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
--------------------------------------------------------------------------------


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_______________________________________________
Bioconductor mailing list
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https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793


---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development&   Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
--------------------------------------------------------------------------------


[[alternative HTML version deleted]]




_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org<mailto:Bioconductor@r-project.org><mailto:Bioconductor@r-project.org>
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793


---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development&  Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk><mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
--------------------------------------------------------------------------------


[[alternative HTML version deleted]]




_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org<mailto:Bioconductor@r-project.org>
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor


--
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793


---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development & Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
--------------------------------------------------------------------------------


[[alternative HTML version deleted]]

_______________________________________________
Bioconductor mailing list
Bioconductor@r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

---------------------------------------------------------------------------------
Francesco Lescai, PhD, EDBT
Senior Research Associate in Genome Analysis
University College London
Faculty of Population Health Sciences
Dept. Genes, Development & Disease
ICH - Molecular Medicine Unit, GOSgene team
30 Guilford Street
WC1N 1EH London UK

email: f.lescai@ucl.ac.uk<mailto:f.lescai@ucl.ac.uk>
phone: +44.(0)207.905.2274
[ext: 2274]
--------------------------------------------------------------------------------


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