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
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