This page was generated on 2021-05-06 12:30:35 -0400 (Thu, 06 May 2021).
R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
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> library(testthat)
> library(dasper)
>
> test_check("dasper")
[1] "# Filtering junctions -----------------------------------------------------"
[1] "2021-05-06 02:07:02 - Filtering junctions..."
[1] "2021-05-06 02:07:02 - done!"
[1] "# Annotating junctions ----------------------------------------------------"
[1] "2021-05-06 02:07:02 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-05-06 02:07:34 - Getting junction annotation using overlapping exons..."
[1] "2021-05-06 02:07:36 - Tidying junction annotation..."
[1] "2021-05-06 02:07:36 - Deriving junction categories..."
[1] "2021-05-06 02:07:37 - done!"
[1] "# Normalise junctions -----------------------------------------------------"
[1] "2021-05-06 02:07:37 - Clustering junctions..."
[1] "2021-05-06 02:07:37 - Normalising junction counts..."
[1] "2021-05-06 02:07:37 - done!"
[1] "# Score junctions ---------------------------------------------------------"
[1] "2021-05-06 02:07:37 - Calculating the direction of change of junctions..."
[1] "2021-05-06 02:07:38 - Generating junction abnormality score..."
[1] "2021-05-06 02:07:38 - done!"
[1] "2021-05-06 02:08:05 - Loading junctions for sample 1/1..."
[1] "2021-05-06 02:08:05 - Adding control junctions..."
[1] "2021-05-06 02:08:05 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-05-06 02:08:05 - done!"
[1] "2021-05-06 02:08:05 - Loading junctions for sample 1/2..."
[1] "2021-05-06 02:08:05 - Loading junctions for sample 2/2..."
[1] "2021-05-06 02:08:05 - Adding control junctions..."
[1] "2021-05-06 02:08:05 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-05-06 02:08:05 - done!"
[1] "2021-05-06 02:08:05 - Loading junctions for sample 1/2..."
[1] "2021-05-06 02:08:05 - Loading junctions for sample 2/2..."
[1] "2021-05-06 02:08:05 - Adding control junctions..."
[1] "2021-05-06 02:08:05 - Downloading and importing fibroblasts junction data..."
[1] "2021-05-06 02:08:39 - Tidying and storing junction data as a RangedSummarizedExperiment..."
[1] "2021-05-06 02:08:40 - done!"
[1] "2021-05-06 02:08:40 - Loading junctions for sample 1/2..."
[1] "2021-05-06 02:08:40 - Loading junctions for sample 2/2..."
[1] "2021-05-06 02:08:40 - Adding control junctions..."
[1] "2021-05-06 02:08:40 - Loading junctions for sample 1/2..."
[1] "2021-05-06 02:08:40 - Loading junctions for sample 2/2..."
[1] "2021-05-06 02:08:40 - Adding control junctions..."
[1] "2021-05-06 02:08:40 - Loading junctions for sample 1/2..."
[1] "2021-05-06 02:08:40 - Loading junctions for sample 2/2..."
[1] "2021-05-06 02:08:40 - Adding control junctions..."
[1] "2021-05-06 02:08:56 - Obtaining co-ordinates of annotated exons and junctions from gtf/gff3..."
[1] "2021-05-06 02:09:24 - Filtering junctions..."
[1] "2021-05-06 02:09:24 - by count..."
[1] "2021-05-06 02:09:24 - done!"
[1] "2021-05-06 02:09:24 - Filtering junctions..."
[1] "2021-05-06 02:09:24 - by width..."
[1] "2021-05-06 02:09:24 - done!"
[1] "2021-05-06 02:09:25 - Filtering junctions..."
[1] "2021-05-06 02:09:25 - by type..."
[1] "2021-05-06 02:09:25 - done!"
[1] "2021-05-06 02:09:25 - Filtering junctions..."
[1] "2021-05-06 02:09:25 - by overlap with regions..."
[1] "2021-05-06 02:09:25 - done!"
[1] "2021-05-06 02:09:25 - Filtering junctions..."
[1] "2021-05-06 02:09:25 - by count..."
[1] "2021-05-06 02:09:25 - by width..."
[1] "2021-05-06 02:09:25 - by type..."
[1] "2021-05-06 02:09:25 - by overlap with regions..."
[1] "2021-05-06 02:09:25 - done!"
[1] "2021-05-06 02:09:30 - Clustering junctions..."
[1] "2021-05-06 02:09:30 - Filtering junctions..."
[1] "2021-05-06 02:09:30 - by count..."
[1] "2021-05-06 02:09:30 - done!"
[1] "2021-05-06 02:09:30 - Normalising junction counts..."
[1] "2021-05-06 02:09:31 - done!"
[1] "2021-05-06 02:09:31 - Calculating the direction of change of junctions..."
[1] "2021-05-06 02:09:31 - Generating junction abnormality score..."
[1] "2021-05-06 02:09:31 - done!"
[1] "2021-05-06 02:09:45 - generating outlier scores for sample 1/2"
[1] "2021-05-06 02:09:59 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-05-06 02:10:00 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-05-06 02:10:01 - generating outlier scores for sample 2/2"
[1] "2021-05-06 02:10:01 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-05-06 02:10:02 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-05-06 02:10:03 - done!"
[1] "2021-05-06 02:10:03 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-05-06 02:10:04 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-05-06 02:10:57 - Filtering junctions..."
[1] "2021-05-06 02:10:57 - by count..."
[1] "2021-05-06 02:10:57 - done!"
building whole annotation region map done
2 chromosomes for annotated regions read
Processing C:\Users\BIOCBU~1\AppData\Local/BiocFileCache/BiocFileCache/Cache/c58582431b_SRR660824_SRS389722_SRX222703_male_lung.bw
building whole annotation region map done
2 chromosomes for annotated regions read
Processing C:\Users\BIOCBU~1\AppData\Local/BiocFileCache/BiocFileCache/Cache/c58582431b_SRR660824_SRS389722_SRX222703_male_lung.bw
[1] "2021-05-06 02:11:19 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[1] "2021-05-06 02:11:20 - fitting outlier detection model with parameters: behaviour=deprecated, bootstrap=FALSE, contamination=auto, max_features=1, max_samples=auto, n_estimators=100, n_jobs=NULL, random_state=32, verbose=0, warm_start=FALSE"
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 212 ]
>
> proc.time()
user system elapsed
219.37 10.50 299.67