Errors In Constructing SYSargs2 object

[dnchenchen]

Hi, thanks for your package, it's helpful for me.

But I got an error when I follow your RIBO-Seq Workflow Template.

I run this codes in R: targetspath <- system.file("extdata", "targetsPE.txt", package="systemPipeR") targets <- read.delim(targetspath, comment.char = "#")[, 1:4]
dir_path <- system.file("extdata/cwl/preprocessReads/trim-pe",package = "systemPipeR")
trim <- loadWorkflow(targets = targetspath, wf_file = "trim-pe.cwl", input_file = "trim-pe.yml", dir_path = dir_path) trim <- renderWF(trim, inputvars = c(FileName1 = "_FASTQPATH1", FileName2 = "_FASTQPATH2", SampleName = "SampleName"))

And I got this error: Error in if (basecommand[1] == "mkdir") { : argument is of length zero

Could you help me find the answer here? Thank you!

[dcassol]

Hi @dnchenchen, Thank you for using systemPipeR!

Could you please provide the output of sessionInfo() executed in an R session right after the error occurred?

[dnchenchen]

Here are the output of sessionInfo() :

sessionInfo() R version 4.1.0 (2021-05-18) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale: [1] LC_COLLATE=Chinese (Simplified)_China.936 LC_CTYPE=Chinese (Simplified)_China.936
[3] LC_MONETARY=Chinese (Simplified)_China.936 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.936

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

other attached packages: [1] systemPipeRdata_1.20.0 systemPipeR_1.26.2 ShortRead_1.50.0 GenomicAlignments_1.28.0
[5] SummarizedExperiment_1.22.0 Biobase_2.52.0 MatrixGenerics_1.4.0 matrixStats_0.59.0
[9] BiocParallel_1.26.0 Rsamtools_2.8.0 Biostrings_2.60.1 XVector_0.32.0
[13] GenomicRanges_1.44.0 GenomeInfoDb_1.28.0 IRanges_2.26.0 S4Vectors_0.30.0
[17] BiocGenerics_0.38.0

loaded via a namespace (and not attached): [1] colorspace_2.0-1 rjson_0.2.20 hwriter_1.3.2 ellipsis_0.3.2
[5] rstudioapi_0.13 remotes_2.4.0 bit64_4.0.5 AnnotationDbi_1.54.1
[9] fansi_0.5.0 xml2_1.3.2 splines_4.1.0 cachem_1.0.5
[13] jsonlite_1.7.2 annotate_1.70.0 GO.db_3.13.0 dbplyr_2.1.1
[17] png_0.1-7 pheatmap_1.0.12 graph_1.70.0 compiler_4.1.0
[21] httr_1.4.2 GOstats_2.58.0 backports_1.2.1 assertthat_0.2.1
[25] Matrix_1.3-4 fastmap_1.1.0 limma_3.48.0 prettyunits_1.1.1
[29] tools_4.1.0 gtable_0.3.0 glue_1.4.2 GenomeInfoDbData_1.2.6
[33] Category_2.58.0 dplyr_1.0.7 rsvg_2.1.2 batchtools_0.9.15
[37] rappdirs_0.3.3 tinytex_0.32 V8_3.4.2 Rcpp_1.0.6
[41] vctrs_0.3.8 rtracklayer_1.52.0 xfun_0.23 stringr_1.4.0
[45] lifecycle_1.0.0 restfulr_0.0.13 XML_3.99-0.6 edgeR_3.34.0
[49] zlibbioc_1.38.0 scales_1.1.1 BSgenome_1.60.0 VariantAnnotation_1.38.0 [53] hms_1.1.0 RBGL_1.68.0 RColorBrewer_1.1-2 yaml_2.2.1
[57] curl_4.3.1 memoise_2.0.0 ggplot2_3.3.4 biomaRt_2.48.1
[61] latticeExtra_0.6-29 stringi_1.6.1 RSQLite_2.2.7 genefilter_1.74.0
[65] BiocIO_1.2.0 checkmate_2.0.0 GenomicFeatures_1.44.0 filelock_1.0.2
[69] DOT_0.1 rlang_0.4.11 pkgconfig_2.0.3 bitops_1.0-7
[73] lattice_0.20-44 purrr_0.3.4 bit_4.0.4 tidyselect_1.1.1
[77] GSEABase_1.54.0 AnnotationForge_1.34.0 magrittr_2.0.1 R6_2.5.0
[81] generics_0.1.0 base64url_1.4 DelayedArray_0.18.0 DBI_1.1.1
[85] pillar_1.6.1 withr_2.4.2 survival_3.2-11 KEGGREST_1.32.0
[89] RCurl_1.98-1.3 tibble_3.1.2 crayon_1.4.1 utf8_1.2.1
[93] BiocFileCache_2.0.0 jpeg_0.1-8.1 progress_1.2.2 locfit_1.5-9.4
[97] grid_4.1.0 data.table_1.14.0 blob_1.2.1 Rgraphviz_2.36.0
[101] digest_0.6.27 xtable_1.8-4 brew_1.0-6 munsell_0.5.0

[dcassol]

Hello @dnchenchen, Thank you for bringing this to my attention. Could you please install the lasted version? Maybe take a few days to get to Bioconductor, so you can install as follows:

devtools::install_github("tgirke/systemPipeR", ref="RELEASE_3_13")

Thank you! All the best, Daniela