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JEFworks-Lab / HoneyBADGER

HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
http://jef.works/HoneyBADGER/
GNU General Public License v3.0
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Hi #15

Closed 1583767448 closed 5 years ago

1583767448 commented 5 years ago

Sorry to bother you,thanks for developing and maintaining HoneyBADGER! I get the following error when running the code and I can't find the reason.[I am repeating your work]

library("coda", lib.loc="E:/R-3.5.1/library") library("rjags", lib.loc="E:/R-3.5.1/library") Linked to JAGS 4.0.0 Loaded modules: basemod,bugs results <- calcAlleleCnvProb(allele.mats$r.maf, allele.mats$n.sc,

  • allele.mats$l.maf, allele.mats$n.bulk, allele.mats$snps, geneFactor,
  • region=GenomicRanges::GRanges('chr10', IRanges::IRanges(0,1e9)), verbose=TRUE) Assessing posterior probability of CNV in region ... with 69 snps ... within 50 genes ... converting to multi-dimensional arrays ... Aggregating data to list ... Running model ... Compiling model graph

Error in rjags::jags.model(modelFile, data = data, n.chains = 4, n.adapt = 100, : Can't initialize. No nodes in graph. Have you compiled the model?

In addition: There were 12 warnings (use warnings() to see them) Thank you!

JEFworks commented 5 years ago

Hi,

Can you please post the output of warnings() and also your sessionInfo()

As well as the output of:

system.file("bug", "snpModel.bug", package = "HoneyBADGER")

Best, Jean

1583767448 commented 5 years ago

Thanks for your reply!

warnings() 警告信息： 1: In file(modfile, "rt") : file("") only supports open = "w+" and open = "w+b": using the former 2: In file(con, "r") : file("") only supports open = "w+" and open = "w+b": using the former 3: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "l" in data 4: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "r" in data 5: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "n.bulk" in data 6: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "n.sc" in data 7: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "J" in data 8: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "K" in data 9: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "I.j" in data 10: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "pseudo" in data 11: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Unused variable "mono" in data 12: In rjags::jags.model(modelFile, data = data, n.chains = 4, ... : Failed to open file Nothing to compile

sessionInfo() R version 3.5.1 (2018-07-02) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_People's Republic of China.936 [2] LC_CTYPE=Chinese (Simplified)_People's Republic of China.936
[3] LC_MONETARY=Chinese (Simplified)_People's Republic of China.936 [4] LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_People's Republic of China.936

attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base

other attached packages: [1] rjags_4-7 coda_0.19-2
[3] gridExtra_2.3 ChIPseeker_1.16.1
[5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 GenomicFeatures_1.32.3
[7] AnnotationDbi_1.42.1 Biobase_2.40.0
[9] GenomicRanges_1.32.7 GenomeInfoDb_1.16.0
[11] IRanges_2.14.12 S4Vectors_0.18.3
[13] BiocGenerics_0.26.0 HiddenMarkov_1.8-11

loaded via a namespace (and not attached): [1] bitops_1.0-6 matrixStats_0.54.0 enrichplot_1.0.2 bit64_0.9-7
[5] RColorBrewer_1.1-2 progress_1.2.0 httr_1.3.1 UpSetR_1.3.3
[9] tools_3.5.1 R6_2.3.0 KernSmooth_2.23-15 DBI_1.0.0
[13] lazyeval_0.2.1 colorspace_1.3-2 tidyselect_0.2.5 prettyunits_1.0.2
[17] bit_1.1-14 compiler_3.5.1 DelayedArray_0.6.6 rtracklayer_1.40.6
[21] caTools_1.17.1.1 scales_1.0.0 ggridges_0.5.1 stringr_1.3.1
[25] digest_0.6.18 Rsamtools_1.32.3 DOSE_3.6.1 XVector_0.20.0
[29] pkgconfig_2.0.2 plotrix_3.7-4 rlang_0.2.2 rstudioapi_0.8
[33] RSQLite_2.1.1 bindr_0.1.1 farver_1.0 gtools_3.8.1
[37] BiocParallel_1.14.2 GOSemSim_2.6.2 dplyr_0.7.7 RCurl_1.95-4.11
[41] magrittr_1.5 GO.db_3.6.0 GenomeInfoDbData_1.1.0 Matrix_1.2-14
[45] Rcpp_0.12.19 munsell_0.5.0 viridis_0.5.1 yaml_2.2.0
[49] stringi_1.1.7 ggraph_1.0.2 MASS_7.3-51 SummarizedExperiment_1.10.1 [53] zlibbioc_1.26.0 gplots_3.0.1 plyr_1.8.4 qvalue_2.12.0
[57] grid_3.5.1 blob_1.1.1 gdata_2.18.0 ggrepel_0.8.0
[61] DO.db_2.9 crayon_1.3.4 lattice_0.20-35 cowplot_0.9.3
[65] Biostrings_2.48.0 splines_3.5.1 hms_0.4.2 pillar_1.3.0
[69] fgsea_1.6.0 igraph_1.2.2 boot_1.3-20 reshape2_1.4.3
[73] biomaRt_2.36.1 fastmatch_1.1-0 XML_3.98-1.16 glue_1.3.0
[77] data.table_1.11.8 tweenr_1.0.0 gtable_0.2.0 purrr_0.2.5
[81] assertthat_0.2.0 ggplot2_3.0.0 gridBase_0.4-7 ggforce_0.1.3
[85] viridisLite_0.3.0 tibble_1.4.2 GenomicAlignments_1.16.0 memoise_1.1.0
[89] units_0.6-1 bindrcpp_0.2.2

system.file("bug","snpModel.bug",package="HoneyBADGER") [1] ""

Best, Emma

JEFworks commented 5 years ago

Hi Emma,

It looks like the bugs models are not being loaded properly. The output of system.file("bug","snpModel.bug",package="HoneyBADGER") should be something like:

> library(HoneyBADGER)
> system.file("bug","snpModel.bug",package="HoneyBADGER")
[1] "/Library/Frameworks/R.framework/Versions/3.3/Resources/library/HoneyBADGER/bug/snpModel.bug”

Can you double check that HoneyBADGER is properly loaded:

library(HoneyBADGER)
?HoneyBADGER

Do you happen to know where your R packages are installed? Can you check that there is a file called /bug/snpModel.bug in the installed HoneyBADGER directory?

Best, Jean

1583767448 commented 5 years ago

require(devtools) 载入需要的程辑包：devtools devtools::install_github('JEFworks/HoneyBADGER') Downloading GitHub repo JEFworks/HoneyBADGER@master Error in untar2(tarfile, files, list, exdir) : incomplete block on file

1583767448 commented 5 years ago

Hi,Jane The code works for me now. A thousand thanks for your patience.

Have a nice day! Emma