[Bioc-devel] error while trying to run BiocCheck

Martin Morgan martin.morgan at roswellpark.org
Sun Mar 4 00:57:00 CET 2018



On 03/03/2018 06:45 AM, Claris Baby via Bioc-devel wrote:
> Dear all,I am trying to build a package for RNA-seq analysis combining different existing packages in bioconductor and am facing problem while trying to run
> 
> BiocCheck("/home/package_name", `no-check-vignettes`=TRUE)
> The error generated is as follows:
> This is BiocCheck version 1.14.0. BiocCheck is a work in progress. Output and severity of issues may
> change. Installing package...
> * Checking for version number mismatch...
> * Checking if other packages can import this one...
> * Checking to see if we understand object initialization...
>      * NOTE: Consider clarifying how 2 object(s) are initialized. Maybe they are part of a data set
>        loaded with data(), or perhaps part of an object referenced in with() or within().
>      object (function)
>        DataFrame (gene_exp)
>        count (gene_exp)
> Error in dots[["no-check-vignettes"]] : subscript out of bounds

This seems like a bug in BiocCheck; to invoke interactively, use

   BiocCheck("/home/package_name", list(`no-check-vignettes`=TRUE))

or from the command line

   R CMD BiocCheck --no-check-vignettes /home/package_name

We'll try to address the problem shortly...

Martin

> I have already added VignetteBuilder: knitr and Suggests: knitrIt would be very helpful if you could help solve this error and also the note mentioned above....
> 
> Session infoR version 3.4.0 (2017-04-21)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.2 LTS
> 
> Matrix products: default
> BLAS: /usr/lib/libblas/libblas.so.3.6.0
> LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
> 
> locale:
>   [1] LC_CTYPE=en_IN.UTF-8       LC_NUMERIC=C               LC_TIME=en_IN.UTF-8        LC_COLLATE=en_IN.UTF-8
>   [5] LC_MONETARY=en_IN.UTF-8    LC_MESSAGES=en_IN.UTF-8    LC_PAPER=en_IN.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_IN.UTF-8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
>   [1] newtest_0.1.0              BiocCheck_1.14.0           biocViews_1.46.0           biomaRt_2.32.1
>   [5] knitr_1.19                 Rqc_1.10.2                 ggplot2_2.2.1              GenomicFeatures_1.28.5
>   [9] AnnotationDbi_1.38.2       systemPipeR_1.10.2         ShortRead_1.34.1           GenomicAlignments_1.12.2
> [13] SummarizedExperiment_1.6.5 DelayedArray_0.2.7         matrixStats_0.53.1         Biobase_2.36.2
> [17] BiocParallel_1.10.1        Rsamtools_1.28.0           Biostrings_2.44.2          XVector_0.16.0
> [21] GenomicRanges_1.28.6       GenomeInfoDb_1.12.2        IRanges_2.10.4             S4Vectors_0.14.6
> [25] BiocGenerics_0.22.0
> 
> loaded via a namespace (and not attached):
>    [1] backports_1.1.2               GOstats_2.42.0                Hmisc_4.1-1
>    [4] AnnotationHub_2.8.2           LSD_4.0-0                     plyr_1.8.4
>    [7] lazyeval_0.2.1                GSEABase_1.38.2               splines_3.4.0
>   [10] BatchJobs_1.7                 easyRNASeq_2.12.1             digest_0.6.15
>   [13] BiocInstaller_1.28.0          ensembldb_2.0.4               htmltools_0.3.6
>   [16] GO.db_3.4.1                   gdata_2.18.0                  magrittr_1.5
>   [19] checkmate_1.8.5               memoise_1.1.0                 BBmisc_1.11
>   [22] BSgenome_1.44.2               cluster_2.0.6                 DEXSeq_1.22.0
>   [25] limma_3.32.7                  annotate_1.54.0               colorspace_1.3-2
>   [28] blob_1.1.0                    RCurl_1.95-4.10               graph_1.54.0
>   [31] genefilter_1.58.1             brew_1.0-6                    survival_2.41-3
>   [34] sendmailR_1.2-1               VariantAnnotation_1.22.3      ape_5.0
>   [37] gtable_0.2.0                  zlibbioc_1.22.0               scales_0.5.0
>   [40] DESeq_1.28.0                  pheatmap_1.0.8                vsn_3.44.0
>   [43] DBI_0.7                       edgeR_3.18.1                  Rcpp_0.12.15
>   [46] xtable_1.8-2                  htmlTable_1.11.2              foreign_0.8-69
>   [49] bit_1.1-12                    preprocessCore_1.38.1         Formula_1.2-2
>   [52] intervals_0.15.1              AnnotationForge_1.18.2        getopt_1.20.1
>   [55] htmlwidgets_0.9               httr_1.3.1                    gplots_3.0.1
>   [58] RColorBrewer_1.1-2            acepack_1.4.1                 pkgconfig_2.0.1
>   [61] reshape_0.8.7                 XML_3.98-1.9                  Gviz_1.20.0
>   [64] nnet_7.3-12                   locfit_1.5-9.1                rlang_0.1.6
>   [67] reshape2_1.4.3                munsell_0.4.3                 tools_3.4.0
>   [70] qrqc_1.30.0                   RSQLite_2.0                   evaluate_0.10.1
>   [73] stringr_1.2.0                 yaml_2.1.16                   bit64_0.9-7
>   [76] caTools_1.17.1                AnnotationFilter_1.0.0        ASpli_1.2.3
>   [79] RBGL_1.52.0                   nlme_3.1-131                  mime_0.5
>   [82] genomeIntervals_1.32.0        BiocStyle_2.4.1               compiler_3.4.0
>   [85] rstudioapi_0.7                curl_3.1                      interactiveDisplayBase_1.14.0
>   [88] affyio_1.46.0                 tibble_1.4.2                  statmod_1.4.30
>   [91] geneplotter_1.54.0            stringi_1.1.6                 GenomicFiles_1.12.0
>   [94] lattice_0.20-35               ProtGenerics_1.8.0            Matrix_1.2-12
>   [97] markdown_0.8                  stringdist_0.9.4.6            pillar_1.1.0
> [100] optparse_1.4.4                RUnit_0.4.31                  data.table_1.10.4-3
> [103] bitops_1.0-6                  httpuv_1.3.5                  rtracklayer_1.36.5
> [106] R6_2.2.2                      latticeExtra_0.6-28           affy_1.54.0
> [109] hwriter_1.3.2                 KernSmooth_2.23-15            gridExtra_2.3
> [112] codetools_0.2-15              dichromat_2.0-0               gtools_3.5.0
> [115] DESeq2_1.16.1                 Category_2.42.1               rprojroot_1.3-2
> [118] rjson_0.2.15                  GenomeInfoDbData_0.99.0       grid_3.4.0
> [121] rpart_4.1-12                  rmarkdown_1.8                 biovizBase_1.24.0
> [124] shiny_1.0.5                   base64enc_0.1-3
> 
> Thanking you
> Regards,Claris
> 	[[alternative HTML version deleted]]
> 
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