Search
Question: DiffBind: Error in heights * sapply(called, function(x) x)
0
gravatar for zhaolin20042008
10 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

Zhaolin 

> 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, as.data.frame, cbind, colMeans, colnames,
    colSums, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, lengths, Map, mapply, match,
    mget, order, paste, pmax, pmax.int, pmin, pmin.int, 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:

    expand.grid

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:

    apply

> 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/libblas.so.3
LAPACK: /usr/lib/lapack/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=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   

 

ADD COMMENTlink written 10 months ago by zhaolin200420080
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 210 users visited in the last hour