[Bioc-devel] Resource temporarily unavailable error with rtracklayer

[Vincent Carey]

Can you post an example dataset that triggers the error reproducibly?

On Tue, Jul 14, 2020 at 4:44 AM Charles Plessy <charles.plessy using oist.jp>
wrote:

> Hello,
>
> a user of the CAGEr package reported an error that occurs when it calls
> the `export.bw` function of rtracklayer:
>
> rsession: 1730343 1730344 doesn't intersect 1892288 1899678, chromId 6
> chromSize 5022195: Resource temporarily unavailable
> Error in isSingleString(path) : UCSC library operation failed
> In addition: Warning message:
> In isSingleString(path) : Internal error ucsc/bbiWrite.c 414
>
> This is triggered by a GRanges object that has 236595 lines and 13304
> seqlevels.  My attempts to bisect the object to find a defective line
> did not succeed; but it seems important that I keep most of the contents
> to trigger the error.  I therefore wonder if the problem is either the
> number of lines or the number of seqlevels.
>
> Not being very familiar with the BigWig format and the internals of
> rtracklayer, I am a bit lost.
>
> Can somebody suggest me a way to solve the problem ?
>
> Have a nice day,
>
> Charles
>
> R version 4.0.2 (2020-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Debian GNU/Linux bullseye/sid
>
> Matrix products: default
> BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
> LC_TIME=en_GB.UTF-8
>   [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8
> LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C
>
> [10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats4    stats     graphics  grDevices utils     datasets
>   methods
> [9] base
>
> other attached packages:
>   [1] CAGEr_1.31.3                MultiAssayExperiment_1.15.2
>   [3] SummarizedExperiment_1.19.5 DelayedArray_0.15.6
>   [5] matrixStats_0.56.0          Matrix_1.2-18
>   [7] Biobase_2.49.0              GenomicRanges_1.41.5
>   [9] GenomeInfoDb_1.25.8         IRanges_2.23.10
> [11] S4Vectors_0.27.12           BiocGenerics_0.35.4
>
> loaded via a namespace (and not attached):
>   [1] Rcpp_1.0.5               stringdist_0.9.5.5       lattice_0.20-41
>
>   [4] formula.tools_1.7.1      Rsamtools_2.5.3
> Biostrings_2.57.2
>   [7] gtools_3.8.2             digest_0.6.25            R6_2.4.1
>
> [10] plyr_1.8.6               ggplot2_3.3.2            pillar_1.4.5
>
> [13] zlibbioc_1.35.0          rlang_0.4.7              rstudioapi_0.11
>
> [16] data.table_1.12.8        vegan_2.5-6              splines_4.0.2
>
> [19] BiocParallel_1.23.2      RCurl_1.98-1.2           munsell_0.5.0
>
> [22] compiler_4.0.2           rtracklayer_1.49.3       pkgconfig_2.0.3
>
> [25] mgcv_1.8-31              tidyselect_1.1.0         tibble_3.0.2
>
> [28] GenomeInfoDbData_1.2.3   XML_3.99-0.4             reshape_0.8.8
>
> [31] permute_0.9-5            crayon_1.3.4             dplyr_1.0.0
>
> [34] GenomicAlignments_1.25.3 MASS_7.3-51.6            bitops_1.0-6
>
> [37] grid_4.0.2               nlme_3.1-148             gtable_0.3.0
>
> [40] lifecycle_0.2.0          magrittr_1.5             scales_1.1.1
>
> [43] KernSmooth_2.23-17       stringi_1.4.6            som_0.3-5.1
>
> [46] XVector_0.29.3           ellipsis_0.3.1           generics_0.0.2
>
> [49] vctrs_0.3.1              tools_4.0.2              BSgenome_1.57.4
>
> [52] glue_1.4.1               purrr_0.3.4              colorspace_1.4-1
>
> [55] cluster_2.1.0            operator.tools_1.6.3     beanplot_1.2
>
> [58] memoise_1.1.0            VGAM_1.1-3
>
> --
> Charles Plessy - - ~ ~ ~ ~ ~ ~~~~ ~ ~ ~ ~ ~ - - charles.plessy using oist.jp
> Okinawa  Institute  of  Science  and  Technology  Graduate  University
> Staff scientist in the Luscombe Unit - ~ - https://groups.oist.jp/grsu
> Toots from work - ~ ~~ ~ - https://mastodon.technology/@charles_plessy
>
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