Comments (4)
Hi Sergey, at some point we removed the zscores from the fds assays. It could be that you're using an old FRASER version. Please install the latest one (1.99.0) from our github: https://github.com/gagneurlab/fraser
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Thank you for a response! I've checked my Fraser version and it is old (‘1.12.1’). I've tried to update it with
if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages('BiocManager') BiocManager::install('FRASER')
but got lots of warning messages and several error. Here are mistakes:
Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
namespace 'htmltools' 0.5.5 is being loaded, but >= 0.5.7 is required
Calls: ... withCallingHandlers -> loadNamespace -> namespaceImport -> loadNamespace
Execution halted
ERROR: lazy loading failed for package 'bslib'
Error: package 'DelayedArray' 0.26.6 was found, but >= 0.26.7 is required by 'DelayedMatrixStats'
Execution halted
ERROR: lazy loading failed for package 'DelayedMatrixStats'
I also attach an installation log to this comment.
My OS is Windows 10 and I have R 4.3.1
Thank you very much for your help!
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I also unsuccessfully tried to install Fraser with the same command on Ubuntu web server. Here is a log
Uploading ubuntu_installation_log.txt…
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Hi there,
Seems like you're having some issues updating dependencies while upgrading DROP. Perhaps reinstalling a brand new environment would save a lot of time and effort here. Try starting again with a new environment. Or you could see #509 and try the solution mentioned there by installing using the yml file. This is also detailed in the README.
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Related Issues (20)
- Annotation file asks for columns that shouldn't be needed HOT 2
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 10
- Pipeline fails with no significant results (AberrantSplicing_pipeline_FRASER_08_extract_results_FraseR_R) HOT 1
- Error in rule AberrantSplicing_pipeline_Counting_01_1_countRNA_splitReads_samplewise_R HOT 2
- Pipeline FAILS when specifying subsets of genes to test HOT 1
- useNames = NA is defunct HOT 4
- conda setup using yaml doesn't work HOT 1
- QUESTION: specifying samples for sampleExclusionMask in OUTRIDER HOT 2
- No Overview.html file after aberrantSplicing analysis with DROP v1.4.0 HOT 4
- Can't load fds-object from DROP in R HOT 2
- Results doubts HOT 2
- Error in checkForAndCreateDir HOT 6
- Safe way to rerun crashed pipeline HOT 8
- Error in rule AberrantExpression_pipeline_OUTRIDER_Summary_R HOT 1
- Error in Aberrant Expression Analysis with only external counts HOT 2
- Discrepancy between results_per_junction.tsv and results.tsv files
- How does DROP handle chrX expression HOT 1
- External dataset sequencing variability HOT 4
- Earlier crash for NA values in the SEX column HOT 4
- can't run mae module, error in GENOME column HOT 2
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