DiffBind error with dba.count after update
1
0
Entering edit mode
tgjohnst • 0
@tgjohnst-14344
Last seen 3.6 years ago

My team recently updated our Rstudio server (which involved updating R 3.3.2 to 3.4.1 and building the newest version of all packages including DiffBind - previously 2.2.12, now 2.6.0) and since the update, we have been receiving errors when attempting to run the dba.count() function. Following is the output when running the command on a dba object that was imported using the same process that worked in the previous version. I googled around but can't figure out the origin of the error and was wondering if anyone has any insight into what might be causing it?

> replicate_peaks_lenient_counts <- dba.count(replicate_peaks_lenient, minOverlap=1)
Error: Error processing one or more read files. Check warnings().
In addition: There were 25 warnings (use warnings() to see them)
> warnings()
Warning messages:
1: In mclapply(arglist, fn, ..., mc.preschedule = TRUE, mc.allow.recursive = TRUE) :
  all scheduled cores encountered errors in user code
2:   "croi_count_reads" not resolved from current namespace (DiffBind)
3:   "croi_count_reads" not resolved from current namespace (DiffBind)
4:   "croi_count_reads" not resolved from current namespace (DiffBind)
5:   "croi_count_reads" not resolved from current namespace (DiffBind)
6:   "croi_count_reads" not resolved from current namespace (DiffBind)
7:   "croi_count_reads" not resolved from current namespace (DiffBind)
8:   "croi_count_reads" not resolved from current namespace (DiffBind)
9:   "croi_count_reads" not resolved from current namespace (DiffBind)
10:   "croi_count_reads" not resolved from current namespace (DiffBind)
11:   "croi_count_reads" not resolved from current namespace (DiffBind)
12:   "croi_count_reads" not resolved from current namespace (DiffBind)
13:   "croi_count_reads" not resolved from current namespace (DiffBind)
14:   "croi_count_reads" not resolved from current namespace (DiffBind)
15:   "croi_count_reads" not resolved from current namespace (DiffBind)
16:   "croi_count_reads" not resolved from current namespace (DiffBind)
17:   "croi_count_reads" not resolved from current namespace (DiffBind)
18:   "croi_count_reads" not resolved from current namespace (DiffBind)
19:   "croi_count_reads" not resolved from current namespace (DiffBind)
20:   "croi_count_reads" not resolved from current namespace (DiffBind)
21:   "croi_count_reads" not resolved from current namespace (DiffBind)
22:   "croi_count_reads" not resolved from current namespace (DiffBind)
23:   "croi_count_reads" not resolved from current namespace (DiffBind)
24:   "croi_count_reads" not resolved from current namespace (DiffBind)
25:   "croi_count_reads" not resolved from current namespace (DiffBind)

And below is my sessionInfo():

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  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  methods   base     

other attached packages:
 [1] DiffBind_2.6.0             SummarizedExperiment_1.8.0 DelayedArray_0.4.1         matrixStats_0.52.2         Biobase_2.38.0            
 [6] GenomicRanges_1.30.0       GenomeInfoDb_1.14.0        IRanges_2.12.0             S4Vectors_0.16.0           BiocGenerics_0.24.0       
[11] BiocInstaller_1.28.0      

loaded via a namespace (and not attached):
 [1] Category_2.44.0          bitops_1.0-6             bit64_0.9-7              RColorBrewer_1.1-2       progress_1.1.2          
 [6] Rgraphviz_2.22.0         tools_3.4.1              backports_1.1.1          R6_2.2.2                 KernSmooth_2.23-15      
[11] DBI_0.7                  lazyeval_0.2.1           colorspace_1.3-2         prettyunits_1.0.2        RMySQL_0.10.13          
[16] bit_1.1-12               compiler_3.4.1           sendmailR_1.2-1          graph_1.56.0             rtracklayer_1.38.0      
[21] caTools_1.17.1           scales_0.5.0             checkmate_1.8.5          BatchJobs_1.6            genefilter_1.60.0       
[26] RBGL_1.54.0              stringr_1.2.0            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          limma_3.34.0             rlang_0.1.4             
[36] RSQLite_2.0              BBmisc_1.11              bindr_0.1                GOstats_2.44.0           hwriter_1.3.2           
[41] BiocParallel_1.12.0      gtools_3.5.0             dplyr_0.7.4              RCurl_1.95-4.8           magrittr_1.5            
[46] GO.db_3.4.2              GenomeInfoDbData_0.99.1  Matrix_1.2-11            Rcpp_0.12.13             munsell_0.4.3           
[51] yaml_2.1.14              stringi_1.1.5            edgeR_3.20.1             zlibbioc_1.24.0          gplots_3.0.1            
[56] fail_1.3                 plyr_1.8.4               grid_3.4.1               blob_1.1.0               ggrepel_0.7.0           
[61] gdata_2.18.0             lattice_0.20-35          Biostrings_2.46.0        splines_3.4.1            GenomicFeatures_1.30.0  
[66] annotate_1.56.0          locfit_1.5-9.1           rjson_0.2.15             systemPipeR_1.12.0       biomaRt_2.34.0          
[71] glue_1.2.0               XML_3.98-1.9             ShortRead_1.36.0         latticeExtra_0.6-28      gtable_0.2.0            
[76] amap_0.8-14              assertthat_0.2.0         ggplot2_2.2.1            xtable_1.8-2             survival_2.41-3         
[81] tibble_1.3.4             pheatmap_1.0.8           GenomicAlignments_1.14.0 AnnotationDbi_1.40.0     memoise_1.1.0           
[86] bindrcpp_0.2             brew_1.0-6               GSEABase_1.40.0         
diffbind read counting warning message chromatin atac-seq • 809 views
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0
Entering edit mode

Hi,

Yes, it's broken.  I'll check in a fix ASAP. The rules for registering native routines were tightened up a bit, and the one used by dba.count wasn't (isn't) registered properly.  I'l. post as soon as I check in the fix.  Sorry about that.

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1
Entering edit mode
Gord Brown ▴ 630
@gord-brown-5664
Last seen 5 months ago
United Kingdom

Hi,

I've commited a fix to release and devel, so you should see DiffBind 2.6.1 and 2.7.1 as soon as it gets built. 

Sorry for the inconvenience.

 - Gord

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0
Entering edit mode

Hello,

Any fix for this as of yet?

Cheers,

James

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0
Entering edit mode

Hi,

Your question is slightly confusing.  My previous comment specifically says I've commited a fix, and what version it is.  The windows devel build is failing due do dependencies, as are many other packages; nothing I can do about that.  But release is fine.  Are you still seeing errors with 2.6.1?

 - Gord

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