DiffBind update warnings and running errors

Question

[zhaolin20042008]

Hello, I have been working with DiffBind for 6 months. Recently I got some warnings when I update DiffBind 2.6.1. Then previously worked scripts failed to run in DiffBind 2.6.1. I reinstalled the older version 2.4.8 again,however, dba.count still failed if I chose score=DBA_SCORE_SUMMIT but works if I chose score=DBA_SCORE_RPKM. Since the data from ATAC-seq, I was told score=DBA_SCORE_SUMMIT is recommended. Could anyone help me with the problem? Thanks a lot.

Warning messages:
1: no function found corresponding to methods exports from âDelayedArrayâ for: âacbindâ, âarbindâ
2: no function found corresponding to methods exports from âSummarizedExperimentâ for: âacbindâ, âarbindâ
3: multiple methods tables found for ârglistâ
4: multiple methods tables found for âOntologyâ
5: replacing previous import âAnnotationDbi::Ontologyâ by âBiocGenerics::Ontologyâ when loading âGenomicFeaturesâ
6: In .recacheSubclasses(def@className, def, doSubclasses,  ... :
  undefined subclass "GIntervalTree" of class "GenomicRangesORGenomicRangesList"; definition not updated
7: In .recacheSubclasses(def@className, def, doSubclasses,  ... :
  undefined subclass "GIntervalTree" of class "RangedDataORGenomicRanges"; definition not updated
8: In .recacheSubclasses(def@className, def, doSubclasses,  ... :
  undefined subclass "RangedDataList" of class "RangedDataORRangedDataList"; definition not updated
9: multiple methods tables found for âspaceâ
10: replacing previous import âBiocGenerics::Ontologyâ by âAnnotationDbi::Ontologyâ when loading âannotateâ
11: multiple methods tables found for âOntologyâ
12: replacing previous import âBiocGenerics::Ontologyâ by âAnnotationDbi::Ontologyâ when loading âAnnotationForgeâ

Error Information
> eiff<-dba.count(eiff, minOverlap=12,score=DBA_SCORE_SUMMIT,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_1.6.5
 [3] DelayedArray_0.2.7         matrixStats_0.52.2        
 [5] Biobase_2.36.2             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] edgeR_3.18.1             bit64_0.9-7              splines_3.4.2           
 [4] gtools_3.5.0             assertthat_0.2.0         latticeExtra_0.6-28     
 [7] amap_0.8-14              RBGL_1.52.0              blob_1.1.0              
[10] GenomeInfoDbData_0.99.0  Rsamtools_1.28.0         ggrepel_0.7.0           
[13] Category_2.42.1          RSQLite_2.0              backports_1.1.1         
[16] lattice_0.20-35          glue_1.2.0               limma_3.32.7            
[19] digest_0.6.12            RColorBrewer_1.1-2       XVector_0.16.0          
[22] checkmate_1.8.5          colorspace_1.3-2         Matrix_1.2-12           
[25] plyr_1.8.4               GSEABase_1.38.2          XML_3.98-1.9            
[28] pkgconfig_2.0.1          pheatmap_1.0.8           ShortRead_1.34.1        
[31] biomaRt_2.32.1           genefilter_1.58.1        zlibbioc_1.22.0         
[34] xtable_1.8-2             GO.db_3.4.1              scales_0.5.0            
[37] brew_1.0-6               gdata_2.18.0             BiocParallel_1.10.1     
[40] tibble_1.3.4             annotate_1.54.0          ggplot2_2.2.1           
[43] GenomicFeatures_1.28.5   lazyeval_0.2.0           magrittr_1.5            
[46] survival_2.41-3          memoise_1.1.0            systemPipeR_1.10.2      
[49] fail_1.3                 gplots_3.0.1             hwriter_1.3.2           
[52] GOstats_2.42.0           graph_1.54.0             tools_3.4.2             
[55] BBmisc_1.11              stringr_1.2.0            sendmailR_1.2-1         
[58] munsell_0.4.3            locfit_1.5-9.1           bindrcpp_0.2            
[61] AnnotationDbi_1.38.2     Biostrings_2.44.2        compiler_3.4.2          
[64] caTools_1.17.1           rlang_0.1.4              grid_3.4.2              
[67] RCurl_1.95-4.8           rjson_0.2.15             AnnotationForge_1.18.2  
[70] bitops_1.0-6             base64enc_0.1-3          gtable_0.2.0            
[73] DBI_0.7                  R6_2.2.2                 GenomicAlignments_1.12.2
[76] dplyr_0.7.4              rtracklayer_1.30.4       bit_1.1-12              
[79] bindr_0.1                KernSmooth_2.23-15       stringi_1.1.5           
[82] BatchJobs_1.6            Rcpp_0.12.13

[jared.andrews07]

You'd likely get a quicker response by posting on the Bioconductor forum. The authors are pretty active there.

[zhaolin20042008]

Thanks for suggestion. I will try.