[Bioc-devel] Error in NSBS
Michael Lawrence
lawrence.michael at gene.com
Fri Dec 11 23:15:39 CET 2015
On Fri, Dec 11, 2015 at 2:02 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi,
>
> On 12/11/2015 12:42 PM, Krithika Bhuvaneshwar [kb472 at georgetown.edu] wrote:
>>
>> Thank you for your email.
>>
>> I did fix the issue.
>>
>> The problem was with GenomicRanges in the DESCRIPTION/NAMESPACE file of
>> the package. Initially I listed it in the "imports" section of the
>> DESCRIPTION file, and it looks like the vignette was not picking it up
>> when I tried to build it.
>>
>> So I put it in "depends" section. I also made sure import(GenomicRanges)
>> was added to NAMESPACE. That seemed to fix the issue.
>
I'm guessing that it was adding import(GenomicRanges) to NAMESPACE
that fixed the issue. You should never have to list the package in
Depends to fix symbol resolution.
>
> Good to know.
>
> I'm putting this back on the list where you originally posted this
> so the other the developers know that you've addressed the issue
> and they don't need to spend time trying to help you with this.
>
> Cheers,
> H.
>
>>
>> Thanks !
>>
>>
>>
>> --Krithika
>>
>> ------------------------------------------------------------------------------
>> Ms. Krithika Bhuvaneshwar
>> Bioinformatician/Data Manager
>> Innovation Center for Biomedical Informatics (ICBI),
>> Georgetown University Medical Center, Washington, DC
>> Email: kb472 at georgetown.edu <mailto:kb472 at georgetown.edu> ;
>> krithika.gu at gmail.com <mailto:krithika.gu at gmail.com>
>> Phone: 202-687-6850; Fax: 202-687-5011
>> http://icbi.georgetown.edu/
>>
>> -------------------------------------------------------------------------------
>>
>>
>> On Fri, Dec 11, 2015 at 3:38 PM, Hervé Pagès <hpages at fredhutch.org
>> <mailto:hpages at fredhutch.org>> wrote:
>>
>> 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
>> <mailto: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]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> --
>> 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 <mailto:hpages at fredhutch.org>
>> Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>> Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>
>
> --
> 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
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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