[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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