[Bioc-devel] BiocCheck - warning: files are over 5MB
Dear all,I am trying to run
BiocCheck("/home/package_name", list(`no-check-vignettes`=TRUE))
There is no error but I am getting the following warning.
$warning
[1] "The following files are over 5MB in size:
'dataset/Caenorhabditis_elegans.WBcel235.dna.chromosome.I.fa'."
This as well as other data like .gff files, that are being used for the
reference based assembly are all much more than 5mb.
But the total package size is less than 500mb.
Is it essential that each file within the package is less than 5mb. If so, it
would be very kind if anyone could suggest how to reduce the size of the
genomic data files.
Wating for your valuable suggestions
Thanking you.
With regards,Claris Baby
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[Bioc-devel] error while trying to run BiocCheck
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
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-8LC_MESSAGES=en_IN.UTF-8LC_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] stats4parallel 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_1.10.1Rsamtools_1.28.0 Biostrings_2.44.2
XVector_0.16.0
[21] GenomicRanges_1.28.6 GenomeInfoDb_1.12.2IRanges_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_2.42.0Hmisc_4.1-1
[4] AnnotationHub_2.8.2 LSD_4.0-0 plyr_1.8.4
[7] lazyeval_0.2.1GSEABase_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_1.1.0RCurl_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_1.0.8vsn_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_1.1-12preprocessCore_1.38.1 Formula_1.2-2
[52] intervals_0.15.1 AnnotationForge_1.18.2getopt_1.20.1
[55] htmlwidgets_0.9 httr_1.3.1gplots_3.0.1
[58] RColorBrewer_1.1-2acepack_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_1.5-9.1rlang_0.1.6
[67] reshape2_1.4.3munsell_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_1.17.1AnnotationFilter_1.0.0
[Bioc-devel] warning: checking Rd cross-references
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 Check PackageThere is no error but a warning saying checking Rd cross-references ... WARNING Missing link or links in documentation object 'annotate.Rd': ‘biomaRt’ Missing link or links in documentation object 'countT.Rd': ‘systemPipeR’ See section 'Cross-references' in the 'Writing R Extensions' manual. How can I change this? It would be very helpful if anyone could suggest where I am going wrong and how to correct it.Thanks in advance Warm Regards,Claris [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
