[Bioc-devel] error while trying to run BiocCheck

Claris Baby clarisbaby at yahoo.com
Sat Mar 3 12:45:00 CET 2018

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
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

 [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                 

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
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