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 at 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