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

[Pages, Herve]

Hi Paul,

Is there a possibility that trena's code is having one worker 
downloading/re-installing BSgenome.Hsapiens.UCSC.hg38 while at the same 
time another worker is trying to access it?

The reason I suspect something like this is that it seems that 
BSgenome.Hsapiens.UCSC.hg38 gets reinstalled every night on the builders 
and that this happens at the time the build system is running 'R CMD 
check' on trena.

Package vignettes, examples, and unit tests should avoid re-installing 
packages.

H.

On 4/22/19 15:01, Paul Shannon wrote:
> 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://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_95963_&d=DwIFAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=1AJWecG5cm0EI_BZG7zYbHNZa3JkQY8pdsJFahrtpIU&s=2WHZQbOLmt-jvKlwVBty43jY5JcBt2U_sdqZDqRxEOY&e=
>
> 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
>
> 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] 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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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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