Question: DiffBind: Error in heights * sapply(called, function(x) x)
gravatar for zhaolin20042008
5 months ago by
U of Michigan
zhaolin200420080 wrote:

Hello, Rory, Thank you for suggestions at C: Warnings when update DiffBind and running errors. I still failed run with dba.count, however. Here is what I have done. 

1. I have update all the packages. when loading Diffbind 2.6, there is no warnings.

2. Then I run dba.count using  summits=150 with score default. the error came out again. How could I fix it? 

Error in heights * sapply(called, function(x) x) : non-conformable arrays

Many Thanks


> library(DiffBind)
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: âBiocGenericsâ

The following objects are masked from âpackage:parallelâ:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from âpackage:statsâ:

    IQR, mad, sd, var, xtabs

The following objects are masked from âpackage:baseâ:

    anyDuplicated, append,, cbind, colMeans, colnames,
    colSums,, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax,, pmin,, Position, rank,
    rbind, Reduce, rowMeans, rownames, rowSums, sapply, setdiff, sort,
    table, tapply, union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors

Attaching package: âS4Vectorsâ

The following object is masked from âpackage:baseâ:


Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: âmatrixStatsâ

The following objects are masked from âpackage:Biobaseâ:

    anyMissing, rowMedians

Attaching package: âDelayedArrayâ

The following objects are masked from âpackage:matrixStatsâ:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from âpackage:baseâ:


> eiff<-dba(sampleSheet="090217_3_CD4.csv",config=data.frame(RunParallel=TRUE, reportInit="eiff",AnalysisMethod=DBA_DESEQ2,th=0.05))
​>eiff1<-dba.count(eiff, minOverlap=12,summits=150,readFormat=DBA_READS_DEFAULT, bParallel=eiff$config$RunParallel)
Re-centering peaks...
Error in heights * sapply(called, function(x) x) : non-conformable arrays

> sessionInfo()

R version 3.4.2 (2017-09-28)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/
LAPACK: /usr/lib/lapack/

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] DiffBind_2.6.1             SummarizedExperiment_1.8.0
 [3] DelayedArray_0.4.1         matrixStats_0.52.2        
 [5] Biobase_2.38.0             GenomicRanges_1.30.0      
 [7] GenomeInfoDb_1.14.0        IRanges_2.12.0            
 [9] S4Vectors_0.16.0           BiocGenerics_0.24.0       


loaded via a namespace (and not attached):
 [1] Category_2.44.0          bitops_1.0-6             bit64_0.9-7             
 [4] RColorBrewer_1.1-2       progress_1.1.2           Rgraphviz_2.22.0        
 [7] tools_3.4.2              backports_1.1.1          R6_2.2.2                
[10] KernSmooth_2.23-15       DBI_0.7                  lazyeval_0.2.1          
[13] colorspace_1.3-2         prettyunits_1.0.2        RMySQL_0.10.13          
[16] bit_1.1-12               compiler_3.4.2           sendmailR_1.2-1         
[19] graph_1.56.0             rtracklayer_1.38.0       caTools_1.17.1          
[22] scales_0.5.0             checkmate_1.8.5          BatchJobs_1.7           
[25] genefilter_1.60.0        RBGL_1.54.0              stringr_1.2.0           
[28] digest_0.6.12            Rsamtools_1.30.0         AnnotationForge_1.20.0  
[31] XVector_0.18.0           base64enc_0.1-3          pkgconfig_2.0.1         
[34] limma_3.34.2             rlang_0.1.4              RSQLite_2.0             
[37] BBmisc_1.11              BiocInstaller_1.28.0     bindr_0.1               
[40] GOstats_2.44.0           hwriter_1.3.2            BiocParallel_1.10.1     
[43] gtools_3.5.0             dplyr_0.7.4              RCurl_1.95-4.8          
[46] magrittr_1.5             GO.db_3.5.0              GenomeInfoDbData_0.99.1 
[49] Matrix_1.2-12            Rcpp_0.12.14             munsell_0.4.3

[52] stringi_1.1.6            edgeR_3.18.1             zlibbioc_1.24.0         

[55] gplots_3.0.1             plyr_1.8.4               grid_3.4.2              
[58] blob_1.1.0               ggrepel_0.7.0            gdata_2.18.0            
[61] lattice_0.20-35          Biostrings_2.46.0        splines_3.4.2           
[64] GenomicFeatures_1.30.0   annotate_1.56.1          locfit_1.5-9.1          
[67] rjson_0.2.15             systemPipeR_1.12.0       biomaRt_2.34.0          
[70] glue_1.2.0               XML_3.98-1.9             ShortRead_1.36.0        
[73] latticeExtra_0.6-28      data.table_1.10.4-3      gtable_0.2.0            
[76] amap_0.8-14              assertthat_0.2.0         ggplot2_2.2.1           
[79] xtable_1.8-2             survival_2.41-3          tibble_1.3.4            
[82] pheatmap_1.0.8           GenomicAlignments_1.14.1 AnnotationDbi_1.40.0    
[85] memoise_1.1.0            bindrcpp_0.2             brew_1.0-6              
[88] GSEABase_1.40.1   


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