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Question: Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)
1
gravatar for mdoering
8 months ago by
mdoering10
mdoering10 wrote:

Dear all,

I have just installed the current R development version to verify whether my package works on the newest R release and I've encountered an issue when combining RangedData/IRanges objects. 

 

library(IRanges)

c(IRanges(), IRanges())
Error in c(IRanges(), IRanges()) : 
  could not find symbol "recursive" in environment of the generic function

c(RangedData(), RangedData())

 

The RangedData doc says

Note that the use of ‘RangedData’ and ‘RangedDataList’ objects has
     been discouraged in favor of ‘GRanges’ and ‘GRangesList’ objects
     since BioC 2.12.

so I guess that everyone switch to GRanges now. In this case, could you output a deprecation warning somehow?

 

Thanks for clarification and best

 Matthias

ADD COMMENTlink modified 8 months ago by Martin Morgan ♦♦ 20k • written 8 months ago by mdoering10

I'm guessing something in your package library is out of sync. Might try reinstalling IRanges or its dependencies.

ADD REPLYlink written 8 months ago by Michael Lawrence9.8k

I just switched to GRanges() and the problem persists. I already reinstalled IRanges and the current version seems to be loaded. Here's my session - thanks for having a look :-)
 

R version 3.3.3 RC (2017-02-28 r72298)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

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] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] GenomicRanges_1.26.3 GenomeInfoDb_1.10.3  BiocInstaller_1.24.0
 [4] doParallel_1.0.10    iterators_1.0.8      foreach_1.4.3       
 [7] IRanges_2.8.1        S4Vectors_0.12.1     BiocGenerics_0.20.0 
[10] openPrimeR_0.99.0    DT_0.2               shinyBS_0.61        
[13] shinyjs_0.9          shiny_1.0.0          devtools_1.12.0     
[16] roxygen2_6.0.1      

loaded via a namespace (and not attached):
 [1] jsonlite_1.3          splines_3.3.3         Formula_1.2-1        
 [4] assertthat_0.1        latticeExtra_0.6-28   yaml_2.1.14          
 [7] RSQLite_1.1-2         backports_1.0.5       lattice_0.20-34      
[10] digest_0.6.12         RColorBrewer_1.1-2    XVector_0.14.0       
[13] checkmate_1.8.2       colorspace_1.3-2      htmltools_0.3.5      
[16] httpuv_1.3.3          Matrix_1.2-8          plyr_1.8.4           
[19] XML_3.98-1.5          zlibbioc_1.18.0       xtable_1.8-2         
[22] scales_0.4.1          stringdist_0.9.4.4    htmlTable_1.9        
[25] tibble_1.2            ggplot2_2.2.1         withr_1.0.2          
[28] nnet_7.3-12           lazyeval_0.2.0        survival_2.40-1      
[31] magrittr_1.5          crayon_1.3.2          mime_0.5             
[34] memoise_1.0.0         nlme_3.1-131          xml2_1.1.1           
[37] foreign_0.8-67        tools_3.3.3           data.table_1.10.4    
[40] stringr_1.2.0         V8_1.2                munsell_0.4.3        
[43] cluster_2.0.5         Biostrings_2.42.1     compiler_3.3.3       
[46] ade4_1.7-5            RCurl_1.95-4.8        grid_3.3.3           
[49] htmlwidgets_0.8       miniUI_0.1.1          bitops_1.0-6         
[52] tcltk_3.3.3           base64enc_0.1-3       testthat_1.0.2       
[55] gtable_0.2.0          codetools_0.2-15      curl_2.3             
[58] DBI_0.5-1             sets_1.0-16           reshape2_1.4.2       
[61] R6_2.2.0              lpSolveAPI_5.5.2.0-17 gridExtra_2.2.1      
[64] knitr_1.15.1          seqinr_3.3-3          commonmark_1.2       
[67] Hmisc_4.0-2           ape_4.1               stringi_1.1.2        
[70] Rcpp_0.12.9           DECIPHER_2.2.0        rpart_4.1-10         
[73] acepack_1.4.1   

Best

 Matthias

ADD REPLYlink written 8 months ago by mdoering10
14
gravatar for Martin Morgan
8 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

This is due to an unintentional change introduced into R-3.3.3.  The following Bioconductor packages need to be re-installed. For the next several days, the packages need to be installed 'from source', which for some packages requires tools to compile C and other code. See Windows and Mac-specific instructions; new packages compatible with R-3.3.3 will be available as soon as possible, but perhaps not until after the weekend.

pkgs <- c(
    "S4Vectors", "IRanges", "GenomicRanges", "DelayedArray",
    "XVector", "GenomicAlignments", "ShortRead",
    "VariantAnnotation", "AnnotationHub", "GGtools",
    "ggbio", "ChemmineR", "InteractionSet", "flowCore",
    "GenomicTuples", "CNEr", "MultiAssayExperiment",
    "genomeIntervals", "TFBSTools", "IWTomics", "spliceSites",
    "podkat", "kebabs", "matter", "dada2",
    "ClusterSignificance", "gespeR", "HiTC", "tigre", "soGGi"
)
update <- intersect(rownames(installed.packages()), pkgs)
biocLite(update, type="source", ask=FALSE)

The only alternative is to avoid updating R until the situation is resolved.

ADD COMMENTlink modified 8 months ago • written 8 months ago by Martin Morgan ♦♦ 20k

Thanks a bunch! I thought I already re-installed all of the IRanges dependencies but apparently I didn't. Combining RangeData objects worked after this and combining GRanges also works now after re-installing GenomicRanges too.

 

Best

 Matthias

ADD REPLYlink written 8 months ago by mdoering10

Great, works for me but had to specify type = "source" in order to fix the problem.

ADD REPLYlink modified 8 months ago • written 8 months ago by Diego Diez700
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