[Bioc-devel] Error in NSBS

Hervé Pagès hpages at fredhutch.org
Fri Dec 11 23:02:44 CET 2015


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.

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



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