exomeCopy - no .Internal function 'cov' error
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@lescai-francesco-5078
Last seen 2.6 years ago
Denmark
Hi there, I was trying to update my code after updating the package exomeCopy, but I get an error from the exomeCopy function. Error in var(lmfit$residuals) : there is no .Internal function 'cov' In order to be 100% sure I've followed exactly the vignette code, loading the package data, and I get the very same error > fit <- exomeCopy(rdata["chr1"],sample.name=exome.samples[3],X.names= c("bg","GC","GC.sq","width"),S=0:6,d=2) Error in var(lmfit$residuals) : there is no .Internal function 'cov' or if more than one chromosome > fit.list <- lapply(samples,runExomeCopy,seqs) Error in var(lmfit$residuals) : there is no .Internal function 'cov' I'm using one of the R-devel versions - sessionInfo below thanks very much, Francesco > sessionInfo() R Under development (unstable) (2012-07-02 r59715) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/en_US.UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] multicore_0.1-7 exomeCopy_1.3.1 Rsamtools_1.9.18 Biostrings_2.25.6 GenomicRanges_1.9.28 [6] IRanges_1.15.17 BiocGenerics_0.3.0 loaded via a namespace (and not attached): [1] MASS_7.3-19 RColorBrewer_1.0-5 bitops_1.0-4.1 colorspace_1.1-1 dichromat_1.2-4 [6] digest_0.5.2 ggplot2_0.9.1 grid_2.16.0 labeling_0.1 memoise_0.1 [11] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 reshape2_1.2.1 scales_0.2.1 [16] stats4_2.16.0 stringr_0.6 tools_2.16.0 zlibbioc_1.3.0
exomeCopy exomeCopy • 617 views
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@martin-morgan-1513
Last seen 21 hours ago
United States
On 07/14/2012 09:08 AM, Lescai, Francesco wrote: > Hi there, > I was trying to update my code after updating the package exomeCopy, but I get an error from the exomeCopy function. > > Error in var(lmfit$residuals) : there is no .Internal function 'cov' > > In order to be 100% sure I've followed exactly the vignette code, loading the package data, and I get the very same error > >> fit <- exomeCopy(rdata["chr1"],sample.name=exome.samples[3],X.names =c("bg","GC","GC.sq","width"),S=0:6,d=2) > Error in var(lmfit$residuals) : there is no .Internal function 'cov' > > or if more than one chromosome >> fit.list <- lapply(samples,runExomeCopy,seqs) > Error in var(lmfit$residuals) : there is no .Internal function 'cov' > > I'm using one of the R-devel versions - sessionInfo below One answer is that, to use R-devel, specify type="source" when installing packages, e.g., biocLite('exomeCopy', type='source') This may require that you have additional operating system specific tools installed, as described here http://r.research.att.com/tools/. An alternative, consistent with Bioc builds, is to use R-2.15.1 for devel, as described at http://bioconductor.org/developers/useDevel/. R is now on a yearly release cycle. As a consequence both release and devel versions of Bioconductor are currently built using R-2.15.1 (Bioc-devel will switch to R-devel after our next release, some time in September / October). R-devel has re-organized the location of some .Internal functions, so the R-2.15.1 built packages are not compatible. Martin > > thanks very much, > Francesco > > >> sessionInfo() > R Under development (unstable) (2012-07-02 r59715) > 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] multicore_0.1-7 exomeCopy_1.3.1 Rsamtools_1.9.18 Biostrings_2.25.6 GenomicRanges_1.9.28 > [6] IRanges_1.15.17 BiocGenerics_0.3.0 > > loaded via a namespace (and not attached): > [1] MASS_7.3-19 RColorBrewer_1.0-5 bitops_1.0-4.1 colorspace_1.1-1 dichromat_1.2-4 > [6] digest_0.5.2 ggplot2_0.9.1 grid_2.16.0 labeling_0.1 memoise_0.1 > [11] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 reshape2_1.2.1 scales_0.2.1 > [16] stats4_2.16.0 stringr_0.6 tools_2.16.0 zlibbioc_1.3.0 > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793
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thanks Martin, I've recompiled from source, but I get the same error. It doesn't happen with R2.15. I didn't notice the page on BioC devel: that's definitely a better solution. Thanks for highlighting it. cheers, Francesco On 14 Jul 2012, at 18:30, Martin Morgan wrote: On 07/14/2012 09:08 AM, Lescai, Francesco wrote: Hi there, I was trying to update my code after updating the package exomeCopy, but I get an error from the exomeCopy function. Error in var(lmfit$residuals) : there is no .Internal function 'cov' In order to be 100% sure I've followed exactly the vignette code, loading the package data, and I get the very same error fit <- exomeCopy(rdata["chr1"],sample.name=exome.samples[3],X.names=c( "bg","GC","GC.sq","width"),S=0:6,d=2) Error in var(lmfit$residuals) : there is no .Internal function 'cov' or if more than one chromosome fit.list <- lapply(samples,runExomeCopy,seqs) Error in var(lmfit$residuals) : there is no .Internal function 'cov' I'm using one of the R-devel versions - sessionInfo below One answer is that, to use R-devel, specify type="source" when installing packages, e.g., biocLite('exomeCopy', type='source') This may require that you have additional operating system specific tools installed, as described here http://r.research.att.com/tools/. An alternative, consistent with Bioc builds, is to use R-2.15.1 for devel, as described at http://bioconductor.org/developers/useDevel/. R is now on a yearly release cycle. As a consequence both release and devel versions of Bioconductor are currently built using R-2.15.1 (Bioc-devel will switch to R-devel after our next release, some time in September / October). R-devel has re-organized the location of some .Internal functions, so the R-2.15.1 built packages are not compatible. Martin thanks very much, Francesco sessionInfo() R Under development (unstable) (2012-07-02 r59715) 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] multicore_0.1-7 exomeCopy_1.3.1 Rsamtools_1.9.18 Biostrings_2.25.6 GenomicRanges_1.9.28 [6] IRanges_1.15.17 BiocGenerics_0.3.0 loaded via a namespace (and not attached): [1] MASS_7.3-19 RColorBrewer_1.0-5 bitops_1.0-4.1 colorspace_1.1-1 dichromat_1.2-4 [6] digest_0.5.2 ggplot2_0.9.1 grid_2.16.0 labeling_0.1 memoise_0.1 [11] munsell_0.3 plyr_1.7.1 proto_0.3-9.2 reshape2_1.2.1 scales_0.2.1 [16] stats4_2.16.0 stringr_0.6 tools_2.16.0 zlibbioc_1.3.0 _______________________________________________ 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: Arnold Building M1 B861 Phone: (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]]
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