Error in .order_seqlevels(chrom_sizes[, "chrom"])
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Entering edit mode
Tongjun • 0
@tongjun-24234
Last seen 10 weeks ago
United States

Recently I always met this following when using this code: "annoData <- toGRanges(EnsDb.Hsapiens.v86, feature="gene")" under the version of R/4.0 or R/4.1 with ChIPpeakAnno/3.24.1 to 3.28.0. Do anyone meet the same problem and know how to solve it? Thank you!

The error is : Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE

Try to keep the seqname style consistent.

Try to keep the seqname style consistent.

Code should be placed in three backticks as shown below


library("ChIPpeakAnno")
library(EnsDb.Hsapiens.v86)

> annoData <- toGRanges(EnsDb.Hsapiens.v86, feature="gene")

Error in .order_seqlevels(chrom_sizes[, "chrom"]) : 
  !anyNA(m32) is not TRUE

 Try to keep the seqname style consistent.

 Try to keep the seqname style consistent.
> sessionInfo()
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
[1] C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.16.4         
 [3] AnnotationFilter_1.16.0   GenomicFeatures_1.44.2   
 [5] AnnotationDbi_1.54.1      Biobase_2.52.0           
 [7] ChIPpeakAnno_3.28.0       GenomicRanges_1.44.0     
 [9] GenomeInfoDb_1.28.4       IRanges_2.26.0           
[11] S4Vectors_0.30.2          BiocGenerics_0.38.0      

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.24.0         bitops_1.0-7               
 [3] matrixStats_0.61.0          bit64_4.0.5                
 [5] filelock_1.0.2              progress_1.2.2             
 [7] httr_1.4.2                  InteractionSet_1.20.0      
 [9] tools_4.1.1                 utf8_1.2.2                 
[11] R6_2.5.1                    DBI_1.1.1                  
[13] lazyeval_0.2.2              colorspace_2.0-2           
[15] tidyselect_1.1.1            prettyunits_1.1.1          
[17] bit_4.0.4                   curl_4.3.2                 
[19] compiler_4.1.1              VennDiagram_1.6.20         
[21] graph_1.70.0                formatR_1.11               
[23] xml2_1.3.2                  DelayedArray_0.18.0        
[25] rtracklayer_1.52.1          scales_1.1.1               
[27] RBGL_1.68.0                 rappdirs_0.3.3             
[29] stringr_1.4.0               digest_0.6.28              
[31] Rsamtools_2.8.0             XVector_0.32.0             
[33] pkgconfig_2.0.3             MatrixGenerics_1.4.3       
[35] BSgenome_1.60.0             regioneR_1.24.0            
[37] dbplyr_2.1.1                fastmap_1.1.0              
[39] rlang_0.4.12                rstudioapi_0.13            
[41] RSQLite_2.2.8               BiocIO_1.2.0               
[43] generics_0.1.0              BiocParallel_1.26.2        
[45] dplyr_1.0.7                 RCurl_1.98-1.5             
[47] magrittr_2.0.1              GenomeInfoDbData_1.2.6     
[49] futile.logger_1.4.3         Matrix_1.3-4               
[51] Rcpp_1.0.7                  munsell_0.5.0              
[53] fansi_0.5.0                 lifecycle_1.0.1            
[55] stringi_1.7.5               yaml_2.2.1                 
[57] MASS_7.3-54                 SummarizedExperiment_1.22.0
[59] zlibbioc_1.38.0             BiocFileCache_2.0.0        
[61] grid_4.1.1                  blob_1.2.2                 
[63] crayon_1.4.1                lattice_0.20-45            
[65] splines_4.1.1               Biostrings_2.60.2          
[67] multtest_2.48.0             hms_1.1.1                  
[69] KEGGREST_1.32.0             pillar_1.6.4               
[71] rjson_0.2.20                biomaRt_2.48.3             
[73] futile.options_1.0.1        XML_3.99-0.8               
[75] glue_1.4.2                  lambda.r_1.2.4             
[77] png_0.1-7                   vctrs_0.3.8                
[79] gtable_0.3.0                purrr_0.3.4                
[81] assertthat_0.2.1            cachem_1.0.6               
[83] ggplot2_3.3.5               restfulr_0.0.13            
[85] survival_3.2-13             tibble_3.1.5               
[87] GenomicAlignments_1.28.0    memoise_2.0.0              
[89] ellipsis_0.3.2
ChIPpeakAnno • 346 views
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Entering edit mode
Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 7 weeks ago
United States

Thank you for reporting this. Could you please update your GenomeInfoDb and ensembldb and try that again? Let me know if it still showing the Error.

Jianhong.

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Tongjun • 0
@tongjun-24234
Last seen 10 weeks ago
United States

Thank you for your quick reply, Jianhong. After updating the GenomeInfoDb and ensembldb, it is working now.

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Entering edit mode
@herve-pages-1542
Last seen 4 days ago
Seattle, WA, United States

See this issue: Error in .order_seqlevels(chrom_sizes[, "chrom"]) : !anyNA(m32) is not TRUE

The fix was not ported to BioC 3.13 so make sure to upgrade your installation to BioC 3.14 (released last week).

Cheers,

H.

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Entering edit mode

I see. Thanks!

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