[Bioc-devel] Error in NSBS
Hervé Pagès
hpages at fredhutch.org
Fri Dec 11 21:38:20 CET 2015
Hi Krithika,
NSBS() is the internal helper defined in the S4Vectors package that
takes care of checking and normalizing the supplied subscript when
one tries to subset a Vector derivative (e.g. an Rle, Hits, IRanges,
GRanges, GRangesList, etc...). For example:
> IRanges(1:26, 50, names=letters)[LETTERS]
Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
subscript contains invalid names
It's just saying that the subscript 'i' contains names that are not
valid.
So it seems that in your case a subsetting operation that happens
in run.cin.chr() works just fine when you run run.cin.chr()
interactively but not in the context of knitPDF.
It's hard to know why without having more details.
Could you please run R CMD Stangle on your Rmarkdown file? That will
produce a .R file. Then start R and source this .R file with
source("file_produced_by_R_CMD_Stangle.R" , echo=TRUE).
Then please report the full output you get as well as the output of
sessionInfo() (call this after the source() command terminates).
Please use sessionInfo(), not session_info().
Thanks,
H.
On 12/10/2015 09:27 PM, Krithika Bhuvaneshwar [kb472 at georgetown.edu] wrote:
> Hello,
>
> I am working on creating a package, and have come across an issue.
>
> I have some R code in the "R" folder that works just fine when I test it.
> The code contains a function accepts a GRangesList as input.
>
> I call the function from my Rmarkdown file in the "vignette" folder. When I
> test the "code chunk" from the Rmd file, the function works just fine. But
> when I try to "knitPDF", it gives this error
>
> Error in NSBS(i, x, exact = exact, upperBoundIsStrict = !allow.append) :
> subscript contains invalid names
> Calls: <Anonymous> ... [ -> normalizeSingleBracketSubscript -> NSBS -> NSBS
>
> The code is like this:
> data("grl")
> run.cin.chr(grl.seg = grl) #grl is the GRangesList input
>
> Any help on how to fix this issue is much appreciated.
>
>
> This is my session Info.
>> session_info()
> Session info
> -----------------------------------------------------------------------------------------
> setting value
> version R version 3.2.2 (2015-08-14)
> system x86_64, darwin13.4.0
> ui RStudio (0.99.489)
> language (EN)
> collate en_US.UTF-8
> tz America/New_York
> date 2015-12-10
>
> Packages
> ---------------------------------------------------------------------------------------------
> package * version date source
> acepack 1.3-3.3 2014-11-24 CRAN (R 3.2.0)
> affxparser 1.42.0 2015-10-14 Bioconductor
> affyio 1.40.0 2015-10-14 Bioconductor
> AnnotationDbi * 1.32.2 2015-12-09 Bioconductor
> AnnotationHub * 2.2.2 2015-11-08 Bioconductor
> Biobase * 2.30.0 2015-10-14 Bioconductor
> BiocGenerics * 0.16.1 2015-11-06 Bioconductor
> BiocInstaller 1.20.1 2015-11-18 Bioconductor
> BiocParallel 1.4.0 2015-10-14 Bioconductor
> biomaRt 2.26.1 2015-11-23 Bioconductor
> Biostrings * 2.38.2 2015-11-21 Bioconductor
> biovizBase * 1.18.0 2015-10-14 Bioconductor
> bit 1.1-12 2014-04-09 CRAN (R 3.2.0)
> bitops 1.0-6 2013-08-17 CRAN (R 3.2.0)
> BSgenome 1.38.0 2015-10-14 Bioconductor
> caTools 1.17.1 2014-09-10 CRAN (R 3.2.0)
> CINdex * 0.99.4 2015-12-10 Bioconductor
> cluster 2.0.3 2015-07-21 CRAN (R 3.2.2)
> codetools 0.2-14 2015-07-15 CRAN (R 3.2.2)
> colorspace 1.2-6 2015-03-11 CRAN (R 3.2.0)
> DBI * 0.3.1 2014-09-24 CRAN (R 3.2.0)
> devtools * 1.9.1 2015-09-11 CRAN (R 3.2.0)
> dichromat 2.0-0 2013-01-24 CRAN (R 3.2.0)
> digest 0.6.8 2014-12-31 CRAN (R 3.2.0)
> ff 2.2-13 2014-04-09 CRAN (R 3.2.0)
> foreach 1.4.3 2015-10-13 CRAN (R 3.2.0)
> foreign 0.8-66 2015-08-19 CRAN (R 3.2.0)
> Formula 1.2-1 2015-04-07 CRAN (R 3.2.0)
> futile.logger 1.4.1 2015-04-20 CRAN (R 3.2.0)
> futile.options 1.0.0 2010-04-06 CRAN (R 3.2.0)
> gdata 2.17.0 2015-07-04 CRAN (R 3.2.0)
> GenomeInfoDb * 1.6.1 2015-11-03 Bioconductor
> GenomicAlignments 1.6.1 2015-10-22 Bioconductor
> GenomicFeatures * 1.22.6 2015-12-03 Bioconductor
> GenomicRanges * 1.22.1 2015-11-06 Bioconductor
> ggplot2 1.0.1 2015-03-17 CRAN (R 3.2.0)
> GO.db * 3.2.2 2015-11-12 Bioconductor
> gplots 2.17.0 2015-05-02 CRAN (R 3.2.0)
> graph 1.48.0 2015-10-14 Bioconductor
> gridExtra 2.0.0 2015-07-14 CRAN (R 3.2.0)
> gtable 0.1.2 2012-12-05 CRAN (R 3.2.0)
> gtools 3.5.0 2015-05-29 CRAN (R 3.2.0)
> Hmisc 3.17-0 2015-09-21 CRAN (R 3.2.0)
> Homo.sapiens * 1.3.1 2015-12-09 Bioconductor
> htmltools 0.2.6 2014-09-08 CRAN (R 3.2.0)
> httpuv 1.3.3 2015-08-04 CRAN (R 3.2.0)
> httr 1.0.0 2015-06-25 CRAN (R 3.2.0)
> interactiveDisplayBase 1.8.0 2015-10-14 Bioconductor
> IRanges * 2.4.5 2015-12-08 Bioconductor
> iterators 1.0.8 2015-10-13 CRAN (R 3.2.0)
> KernSmooth 2.23-15 2015-06-29 CRAN (R 3.2.2)
> knitr * 1.11 2015-08-14 CRAN (R 3.2.2)
> lambda.r 1.1.7 2015-03-20 CRAN (R 3.2.0)
> lattice 0.20-33 2015-07-14 CRAN (R 3.2.2)
> latticeExtra 0.6-26 2013-08-15 CRAN (R 3.2.0)
> magrittr 1.5 2014-11-22 CRAN (R 3.2.0)
> MASS 7.3-45 2015-11-10 CRAN (R 3.2.2)
> memoise 0.2.1 2014-04-22 CRAN (R 3.2.0)
> mime 0.4 2015-09-03 CRAN (R 3.2.0)
> munsell 0.4.2 2013-07-11 CRAN (R 3.2.0)
> nnet 7.3-11 2015-08-30 CRAN (R 3.2.0)
> oligo * 1.34.0 2015-10-14 Bioconductor
> oligoClasses * 1.32.0 2015-10-14 Bioconductor
> org.Hs.eg.db * 3.2.3 2015-12-09 Bioconductor
> OrganismDbi * 1.12.0 2015-10-14 Bioconductor
> pd.genomewidesnp.6 * 3.14.1 2015-11-30 Bioconductor
> plyr 1.8.3 2015-06-12 CRAN (R 3.2.0)
> preprocessCore 1.32.0 2015-10-14 Bioconductor
> proto 0.3-10 2012-12-22 CRAN (R 3.2.0)
> R6 2.1.1 2015-08-19 CRAN (R 3.2.0)
> RBGL 1.46.0 2015-10-14 Bioconductor
> RColorBrewer 1.1-2 2014-12-07 CRAN (R 3.2.0)
> Rcpp 0.12.2 2015-11-15 CRAN (R 3.2.2)
> RCurl 1.95-4.7 2015-06-30 CRAN (R 3.2.0)
> reshape2 1.4.1 2014-12-06 CRAN (R 3.2.0)
> rmarkdown 0.8.1 2015-10-10 CRAN (R 3.2.2)
> rpart 4.1-10 2015-06-29 CRAN (R 3.2.2)
> Rsamtools 1.22.0 2015-10-14 Bioconductor
> RSQLite * 1.0.0 2014-10-25 CRAN (R 3.2.0)
> rtracklayer * 1.30.1 2015-10-22 Bioconductor
> S4Vectors * 0.8.4 2015-12-08 Bioconductor
> scales 0.3.0 2015-08-25 CRAN (R 3.2.0)
> shiny 0.12.2 2015-08-05 CRAN (R 3.2.0)
> som 0.3-5 2010-04-07 CRAN (R 3.2.0)
> stringi 1.0-1 2015-10-22 CRAN (R 3.2.0)
> stringr 1.0.0 2015-04-30 CRAN (R 3.2.0)
> SummarizedExperiment 1.0.1 2015-11-06 Bioconductor
> survival 2.38-3 2015-07-02 CRAN (R 3.2.2)
> TxDb.Hsapiens.UCSC.hg18.knownGene * 3.2.2 2015-12-09 Bioconductor
> TxDb.Hsapiens.UCSC.hg19.knownGene * 3.2.2 2015-12-09 Bioconductor
> VariantAnnotation 1.16.4 2015-12-09 Bioconductor
> XML 3.98-1.3 2015-06-30 CRAN (R 3.2.0)
> xtable 1.8-0 2015-11-02 CRAN (R 3.2.0)
> XVector * 0.10.0 2015-10-14 Bioconductor
> yaml 2.1.13 2014-06-12 CRAN (R 3.2.0)
> zlibbioc 1.16.0 2015-10-14 Bioconductor
>
> Thanks,
> --Krithika
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
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>
--
Hervé Pagès
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024
E-mail: hpages at fredhutch.org
Phone: (206) 667-5791
Fax: (206) 667-1319
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