DiffBind error with dba.count after update
1
0
Entering edit mode
tgjohnst • 0
@tgjohnst-14344
Last seen 7.0 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 • 2.3k views
ADD COMMENT
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.

ADD REPLY
1
Entering edit mode
Gord Brown ▴ 670
@gord-brown-5664
Last seen 3.8 years 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

ADD COMMENT
0
Entering edit mode

Hello,

Any fix for this as of yet?

Cheers,

James

ADD REPLY
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

ADD REPLY

Login before adding your answer.

Traffic: 690 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6