Question

Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC)

1

Entering edit mode

mdoering ▴ 20

@mdoering-12332

Last seen 21 months ago

Belgium

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

IRanges • 4.4k views

ADD COMMENT • link updated 7.8 years ago by Martin Morgan 25k • written 7.8 years ago by mdoering ▴ 20

0

Entering edit mode

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

ADD REPLY • link 7.8 years ago Michael Lawrence ★ 11k

0

Entering edit mode

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 REPLY • link 7.8 years ago mdoering ▴ 20

score 16 · Accepted Answer · 2017-03-04

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.