[Bioc-devel] build errors: "Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed"

Paul Shannon p@u|@thurmond@@h@nnon @end|ng |rom gm@||@com
Tue Apr 23 00:01:21 CEST 2019

I cannot reproduce daily build failures found in the trena package by the build system.  The build report shows:

trena RUnit Tests - 86 test functions, 7 errors, 0 failures

ERROR in test_.injectSnp: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_bugInStartEndOfMinusStrandHits: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_findMatchesByChromosomalRegion: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_findMatchesByChromosomalRegion.twoAlternateAlleles: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_findMatchesByMultipleChromosomalRegions: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_getSequence: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed
ERROR in test_noMatch: Error in .seqlengths_TwoBitFile(x) : UCSC library operation failed

This seems similar to a bioc support exchange from two years ago, which may suggest that the build system's BSgenome.Hsapiens.UCSC.hg38 is the locus of the problem.   I offer suggestion very tentatively.     

   support https://support.bioconductor.org/p/95963/

Any suggestions?

 - Paul

sessionInfo()  # from my clean R CMD check
R version 3.6.0 beta (2019-04-11 r76379)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS:   /local/users/pshannon/src/R-beta/lib/libRblas.so
LAPACK: /local/users/pshannon/src/R-beta/lib/libRlapack.so

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
 [1] RPostgreSQL_0.6-2   DBI_1.0.0           RUnit_0.4.32       
 [4] trena_1.5.14        MotifDb_1.22.0      Biostrings_2.48.0  
 [7] XVector_0.20.0      IRanges_2.14.12     S4Vectors_0.18.3   
[10] BiocGenerics_0.26.0 glmnet_2.0-16       foreach_1.4.4      
[13] Matrix_1.2-17      

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.10.1       lassopv_0.2.0                    
 [3] progress_1.2.0                    lattice_0.20-38                  
 [5] rtracklayer_1.40.6                blob_1.1.1                       
 [7] XML_3.98-1.19                     rlang_0.3.4                      
 [9] flare_1.6.0                       BiocParallel_1.14.2              
[11] bit64_0.9-7                       splitstackshape_1.4.8            
[13] matrixStats_0.54.0                GenomeInfoDbData_1.1.0           
[15] stringr_1.4.0                     zlibbioc_1.26.0                  
[17] codetools_0.2-16                  memoise_1.1.0                    
[19] Biobase_2.40.0                    biomaRt_2.36.1                   
[21] GenomeInfoDb_1.16.0               curl_3.3                         
[23] AnnotationDbi_1.42.1              lars_1.2                         
[25] Rcpp_1.0.1                        BSgenome_1.48.0                  
[27] DelayedArray_0.6.6                org.Hs.eg.db_3.6.0               
[29] bit_1.1-14                        Rsamtools_1.32.3                 
[31] BSgenome.Hsapiens.UCSC.hg38_1.4.1 RMySQL_0.10.17                   
[33] hms_0.4.2                         digest_0.6.18                    
[35] stringi_1.4.3                     GenomicRanges_1.32.7             
[37] grid_3.6.0                        tools_3.6.0                      
[39] bitops_1.0-6                      magrittr_1.5                     
[41] RCurl_1.95-4.12                   RSQLite_2.1.1                    
[43] randomForest_4.6-14               crayon_1.3.4                     
[45] vbsr_0.0.5                        pkgconfig_2.0.2                  
[47] MASS_7.3-51.4                     data.table_1.12.2                
[49] prettyunits_1.0.2                 httr_1.4.0                       
[51] assertthat_0.2.1                  iterators_1.0.10                 
[53] R6_2.4.0                          GenomicAlignments_1.16.0         
[55] igraph_1.2.4.1                    compiler_3.6.0

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