Closed H-Qiya closed 3 years ago
Dear @H-Qiya, unfortunately, I can not reproduce your error. Even on Windows, I can not reproduce it. Which version do you use and how did you install it? Could you please try the code below in a fresh session?
You do not need to be an administrator and you set already correctly the working dir. So I'm very curious which version you use.
BiocManager::install("FRASER")
library(FRASER)
sampleTable <- fread(system.file("extdata", "sampleTable.tsv", package = "FRASER", mustWork = TRUE))
bamFiles <- system.file(sampleTable[, bamFile], package = "FRASER", mustWork = TRUE)
sampleTable[, `:=`(bamFile, bamFiles)]
settings<-FraserDataSet(colData=sampleTable,workingDir=tempdir())
settings
BiocManager::valid()
This is run under R 4.0.2 and Bioconductor version 3.11 and FRASER 1.0.2
Hi, @c-mertes ! Thanks a lot for your reply! What is unbelievable is that the Error in "---Bam parameters---" disappeared after copying your code above and running in R studio to reinstall FRASER! Meanwhile, my version is R 4.0.3, Bioconductor 3.12 and FRASER 1.2.0. And the code which reported error last time was copied from FRASER manual pdf. Last time, I ran example data and my data respectively in R as an administrator to avoid the above "---Bam parameters---" error, though it was risky. And this time I ran the same data using FRASER without administrator mode. Then I compared those results and found they are exactly the same (I kept set.seed parameters consistent). Anyway, this error has been fixed, though I didn’t figure out how it is produced deeply in machine, hhh.
Also, I noticed your article has been published on NC the other day(DOI: 10.1038/s41467-020-20573-7). Congratulations on your achievement!!!
Thanks for the feedback and for the congratulations! As it is resolved now, I will close the bug. Please let me know if anything else is going wrong in the future!
Hi, Mr Mertes and your team! I've read your manual and relative literature and found your package really worth a try of best effort! However, when running your example data as well as my own data, I met the same error from the very first step as follows: #######Example data in your manual#######
----------------------- Settings ----------------------- Analysis name: Data Analysis Analysis is strand specific: no Working directory: 'C:\Users\ADMINI~1\AppData\Local\Temp\RtmpQ9cxvH'
-------------------- BAM parameters -------------------- Fri Dec 11 09:26:15 2020: The given working directory 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpw1fLb2/FRASER' does not exists. We will create it. Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'scanBamParam': invalid class “FraserDataSet” object: Make sure we can write to the given working directory ' C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpw1fLb2/FRASER '. In addition: Warning message: In dir.create(object@workingDir, recursive = TRUE) : cannot create dir 'C:\Users\biocbuild', reason 'Permission denied'
When working on my own data, I set my own working directory at the first step, and other script is almost the same. Nonetheless, the same error still exists: #######My own data####### ----------------------- Settings ----------------------- Analysis name: Data Analysis Analysis is strand specific: no Working directory: 'Y:/HCM-newly-sequenced/200820-WGX' -------------------- BAM parameters -------------------- Fri Dec 11 09:51:35 2020: The given working directory 'C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpw1fLb2/FRASER' does not exists. We will create it. Error in h(simpleError(msg, call)) : error in evaluating the argument 'object' in selecting a method for function 'scanBamParam': invalid class “FraserDataSet” object: Make sure we can write to the given working directory ' C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpw1fLb2/FRASER '. In addition: Warning message: In dir.create(object@workingDir, recursive = TRUE) : cannot create dir 'C:\Users\biocbuild', reason 'Permission denied'
Is the working directory completely fixed in ' C:\Users\biocbuild\bbs-3.12-bioc\tmpdir\Rtmpw1fLb2/FRASER ' ? How can I alter it into my own path? Otherwise, must I run R as an administrator? Yet this might lead to unpredictable risk? Looking forward to your reply! Thanks a lot!