Comments (3)
I attach my session info, in case it helps:
sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=es_ES.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=es_ES.UTF-8 LC_NAME=es_ES.UTF-8 LC_ADDRESS=es_ES.UTF-8 LC_TELEPHONE=es_ES.UTF-8
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=es_ES.UTF-8
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 gridExtra_2.3 reshape2_1.4.3 TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.6
[5] GenomicFeatures_1.36.0 AnnotationDbi_1.42.1 VariantAnnotation_1.30.0 Rsamtools_2.0.0
[9] Biostrings_2.52.0 XVector_0.23.2 SummarizedExperiment_1.14.0 DelayedArray_0.10.0
[13] BiocParallel_1.18.0 matrixStats_0.54.0 Biobase_2.40.0 GenomicRanges_1.35.2
[17] GenomeInfoDb_1.19.3 IRanges_2.17.6 S4Vectors_0.21.24 BiocGenerics_0.30.0
[21] HoneyBADGER_0.1 ggsignif_0.5.0 xlsx_0.6.1 ggplot2_3.1.1
[25] reshape_0.8.8 plyr_1.8.4
loaded via a namespace (and not attached):
[1] httr_1.4.0 bit64_0.9-7 assertthat_0.2.1 BiocManager_1.30.4 HiddenMarkov_1.8-11 blob_1.1.1
[7] xlsxjars_0.6.1 BSgenome_1.52.0 GenomeInfoDbData_1.2.1 yaml_2.2.0 progress_1.2.0 pillar_1.3.1
[13] RSQLite_2.1.1 lattice_0.20-38 glue_1.3.1 digest_0.6.18 colorspace_1.4-1 htmltools_0.3.6
[19] Matrix_1.2-17 XML_3.98-1.19 pkgconfig_2.0.2 biomaRt_2.36.1 zlibbioc_1.29.0 purrr_0.3.2
[25] scales_1.0.0 rjags_4-8 tibble_2.1.1 withr_2.1.2 lazyeval_0.2.2 magrittr_1.5
[31] crayon_1.3.4 memoise_1.1.0 evaluate_0.13 tools_3.6.0 prettyunits_1.0.2 hms_0.4.2
[37] stringr_1.4.0 munsell_0.5.0 compiler_3.6.0 caTools_1.17.1.2 rlang_0.3.4 grid_3.6.0
[43] RCurl_1.95-4.12 rstudioapi_0.10 bitops_1.0-6 labeling_0.3 rmarkdown_1.12 gtable_0.3.0
[49] DBI_1.0.0 R6_2.4.0 GenomicAlignments_1.20.0 rtracklayer_1.44.0 knitr_1.22 dplyr_0.8.0.1
[55] bit_1.1-14 rJava_0.9-11 stringi_1.4.3 Rcpp_1.0.1 tidyselect_0.2.5 xfun_0.6
[61] coda_0.19-2
from honeybadger.
Dear Jean,
sorry for insisting. Did you have time for taking a look on this?
Thanks again for all your work.
Best,
Juan L.
from honeybadger.
Hi Juan,
Thanks for your patience. This is on my task list and I will get to it as soon as possible.
My general sense that this error is related to a previously closed issue: #13
There were a number of bugs like these that were fixed in the individual functions like calcAlleleCnvBoundaries()
but were unfortunately not properly ported over to their object analogues ie. hb$calcAlleleCnvBoundaries
- Jean
from honeybadger.
Related Issues (20)
- lt$setGexpDev HOT 1
- Warning in setGeneFactors and error in retestIdentifiedCnvs
- Allele-mode for selecting normal cells HOT 2
- 10X + Honeybadger question HOT 2
- Error in summarizeResults HOT 3
- Error in calcGexpCnvBoundaries when running with numeric chromosome names HOT 1
- Error: subscript contains invalid names HOT 9
- read bam files HOT 4
- Filtering of identified CNVs HOT 2
- speed of running setAlleleMats step
- What is the reason for only including snps in HoneyBADGER? HOT 2
- gene filtering different in HoneyBADGER object HOT 3
- Error: Failed to install 'HoneyBADGER' from GitHub HOT 2
- Showing error when trying Getting_Started.Rmd
- no method for coercing this S4 class to a vector HOT 3
- showing NULL in the step of calcGexpCnvBoundaries - getting started tutorial HOT 12
- Applying bayesian hierarchical model in integrating analyses tutorial
- error in hb$summarizeResults
- Error in summarizeResults for the allele-based approach
- Error in calcCombCnvProb HOT 1
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from honeybadger.