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tgirke / systemPipeR

Project Website:
http://girke.bioinformatics.ucr.edu/systemPipeR
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Error in runWF(sal) #73

Closed pwang24 closed 2 years ago

pwang24 commented 2 years ago

Hello,

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

I run the code in R as following:

library(systemPipeR) systemPipeRdata::genWorkenvir(workflow = "riboseq", mydirname = "riboseq") setwd("riboseq") targetspath <- system.file("extdata", "targetsPE.txt", package = "systemPipeR") targets <- read.delim(targetspath, comment.char = "#")[, 1:4] targets library(systemPipeR) sal <- SPRproject() sal appendStep(sal) <- LineWise(code = {

  • library(systemPipeR)
  • library(rtracklayer)
  • library(GenomicFeatures)
  • library(ggplot2)
  • library(grid)
  • library(BiocParallel)
  • library(DESeq2, quietly = TRUE)
  • library(ape, warn.conflicts = FALSE)
  • library(edgeR)
  • library(biomaRt)
  • library(BBmisc) # Defines suppressAll()
  • library(pheatmap)
  • library(BiocParallel)
  • }, step_name = "load_SPR") appendStep(sal) <- SYSargsList(step_name = "preprocessing", targets = "targetsPE.txt",
  • dir = TRUE, wf_file = "preprocessReads/preprocessReads-pe.cwl",
  • input_file = "preprocessReads/preprocessReads-pe_riboseq.yml",
  • dir_path = system.file("extdata/cwl", package = "systemPipeR"),
  • inputvars = c(FileName1 = "_FASTQPATH1", FileName2 = "_FASTQPATH2",
  • SampleName = "SampleName"), dependency = c("load_SPR")) sal <- runWF(sal) But I got the errors like this: Running Step: load_SPR Running Session: Management | | 0%Loading required package: AnnotationDbi

Attaching package: ‘grid’

The following object is masked from ‘package:Biostrings’:

pattern

Attaching package: ‘DESeq2’

The following object is masked from ‘package:systemPipeR’:

results

|=======================================================================================================================| 100% Error in runWF(sal) : Caught an error, stop workflow!

Could you please help me to find the answer? Thank you!

tgirke commented 2 years ago

Unless I overlooked a typo in your code, I am not able to reproduce your error when using the corresponding code from the vignette here. Perhaps check whether all the libraries/packages that are loaded in the first code chunk you showing are indeed installed on your system. If any is missing then this could trigger such an error. If so more explicit error message could be triggered in the future. If this doesn't fix it then make sure you have the latest R/Bioc version and packages installed on your system. If you need more help then it would be import to send the output of sessionInfo() executed right after experiencing the error.

Please note that you can run the workflow without going through the individual steps in its entirety like this:

sal <- importWF(sal, file_path = "systemPipeRIBOseq.Rmd")
runWF(sal)

Instructions on this are in the main vignette here.