estepi
commented
3 years ago Hi, I'm sorry for the delay.
Can you try to run with core=1 and see what happens?
Tomorrow there will be a new release of Bioconductor and ASpli will be updated to v 2.0
maybe, you can download it and try with a lot if improvements
Thanks
ipatop
Hi,
I encountered this issue when running readCounts function, I am now following this manual: https://bioconductor.org/packages/release/bioc/vignettes/ASpli/inst/doc/ASpli.pdf particularly the Example data section but with my own data.
Thanks in advance,
Error:
counts.brainact <- readCounts( features, bam, targets, readLength = 150,
Error in as.data.frame.default(x[[i]], optional = TRUE, stringsAsFactors = stringsAsFactors) : cannot coerce class '"try-error"' to a data.frame In addition: Warning message: In mclapply(reads, mc.cores = cores, function(x) { : scheduled core 1 encountered error in user code, all values of the job will be affected
this is my session info
Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding
locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages: [1] stats4 parallel stats graphics grDevices utils datasets methods base
other attached packages: [1] GenomicFeatures_1.36.4 AnnotationDbi_1.46.1 Biobase_2.44.0 GenomicRanges_1.36.1 GenomeInfoDb_1.20.0
[6] IRanges_2.18.3 S4Vectors_0.22.1 BiocGenerics_0.30.0 ASpli_1.10.0 edgeR_3.26.8
[11] limma_3.40.6
loaded via a namespace (and not attached): [1] backports_1.1.10 Hmisc_4.4-1 fastmatch_1.1-0 plyr_1.8.6
[5] igraph_1.2.6 lazyeval_0.2.2 splines_3.6.1 BiocParallel_1.18.1
[9] ggplot2_3.3.2 urltools_1.7.3 digest_0.6.25 ensembldb_2.8.1
[13] htmltools_0.5.0 GOSemSim_2.10.0 viridis_0.5.1 GO.db_3.8.2
[17] magrittr_1.5 checkmate_2.0.0 memoise_1.1.0 BSgenome_1.52.0
[21] cluster_2.1.0 Biostrings_2.52.0 graphlayouts_0.7.0 matrixStats_0.57.0
[25] enrichplot_1.4.0 prettyunits_1.1.1 jpeg_0.1-8.1 colorspace_1.4-1
[29] blob_1.2.1 ggrepel_0.8.2 xfun_0.18 dplyr_1.0.2
[33] crayon_1.3.4 RCurl_1.98-1.2 jsonlite_1.7.1 VariantAnnotation_1.30.1
[37] survival_3.2-7 glue_1.4.2 polyclip_1.10-0 gtable_0.3.0
[41] zlibbioc_1.30.0 XVector_0.24.0 UpSetR_1.4.0 DelayedArray_0.10.0
[45] scales_1.1.1 DOSE_3.10.2 DBI_1.1.0 Rcpp_1.0.5
[49] viridisLite_0.3.0 progress_1.2.2 htmlTable_2.1.0 gridGraphics_0.5-0
[53] foreign_0.8-76 bit_4.0.4 europepmc_0.4 Formula_1.2-3
[57] htmlwidgets_1.5.2 httr_1.4.2 fgsea_1.10.1 RColorBrewer_1.1-2
[61] ellipsis_0.3.1 pkgconfig_2.0.3 XML_3.99-0.3 farver_2.0.3
[65] Gviz_1.28.3 nnet_7.3-14 locfit_1.5-9.4 ggplotify_0.0.5
[69] tidyselect_1.1.0 rlang_0.4.8 reshape2_1.4.4 munsell_0.5.0
[73] tools_3.6.1 generics_0.0.2 RSQLite_2.2.1 ggridges_0.5.2
[77] evaluate_0.14 stringr_1.4.0 yaml_2.2.1 knitr_1.30
[81] bit64_4.0.5 tidygraph_1.2.0 purrr_0.3.4 AnnotationFilter_1.8.0
[85] ggraph_2.0.3 DO.db_2.9 xml2_1.3.2 biomaRt_2.40.5
[89] BiocStyle_2.12.0 compiler_3.6.1 rstudioapi_0.11 curl_4.3
[93] png_0.1-7 tibble_3.0.4 tweenr_1.0.1 stringi_1.5.3
[97] lattice_0.20-41 ProtGenerics_1.16.0 Matrix_1.2-18 vctrs_0.3.4
[101] pillar_1.4.6 lifecycle_0.2.0 BiocManager_1.30.10 triebeard_0.3.0
[105] data.table_1.12.8 cowplot_1.1.0 bitops_1.0-6 rtracklayer_1.44.4
[109] qvalue_2.16.0 R6_2.4.1 latticeExtra_0.6-29 gridExtra_2.3
[113] dichromat_2.0-0 MASS_7.3-53 SummarizedExperiment_1.14.1 GenomicAlignments_1.20.1
[117] Rsamtools_2.0.3 GenomeInfoDbData_1.2.1 hms_0.5.3 clusterProfiler_3.12.0
[121] grid_3.6.1 rpart_4.1-15 tidyr_1.1.2 rmarkdown_2.4
[125] rvcheck_0.1.8 biovizBase_1.32.0 ggforce_0.3.2 base64enc_0.1-3