| Back to Build/check report for BioC 3.17 |
|
This page was generated on 2023-02-23 01:34:30 -0000 (Thu, 23 Feb 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences" | 4245 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
|
To the developers/maintainers of the SpliceWiz package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceWiz.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1932/2164 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.1.5 (landing page) Alex Chit Hei Wong
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | ERROR | |||||||||
| Package: SpliceWiz |
| Version: 1.1.5 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SpliceWiz_1.1.5.tar.gz |
| StartedAt: 2023-02-22 13:32:13 -0000 (Wed, 22 Feb 2023) |
| EndedAt: 2023-02-22 13:50:05 -0000 (Wed, 22 Feb 2023) |
| EllapsedTime: 1072.5 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/library --timings SpliceWiz_1.1.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SpliceWiz.Rcheck’
* using R Under development (unstable) (2023-01-14 r83615)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.1 LTS
* using session charset: UTF-8
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.1.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpliceWiz’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... NOTE
installed size is 12.1Mb
sub-directories of 1Mb or more:
R 2.0Mb
libs 9.0Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ASE-methods 70.076 0.526 70.601
NxtSE-class 54.962 0.622 55.671
Build-Reference-methods 24.294 0.172 24.468
plotCoverage 11.309 0.139 11.425
ASE-GLM-edgeR 10.503 0.132 10.637
Run_SpliceWiz_Filters 7.562 0.016 7.579
makeSE 6.859 0.031 6.886
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
Feb 22 13:44:17 Iteration 2
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Mappa.R:20'): SpliceWiz pipeline reproduces NxtSE object ───────
Error in `.stop_quietly()`:
Backtrace:
▆
1. └─Rsubread::subjunc(...) at test-Mappa.R:20:4
2. └─Rsubread:::.load.delete.summary(output_file[i])
3. └─Rsubread:::.stop_quietly()
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘SW_Cookbook.Rmd’ using ‘UTF-8’... OK
‘SW_QuickStart.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SpliceWiz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R/library’ * installing *source* package ‘SpliceWiz’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c BAM2blocks.cpp -o BAM2blocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c FastaReader.cpp -o FastaReader.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c FragmentBlocks.cpp -o FragmentBlocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c GZTools.cpp -o GZTools.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c covTools.cpp -o covTools.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c main.cpp -o main.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c swEngine.cpp -o swEngine.o g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.17-bioc/R/library/ompBAM/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/zlibbioc/include' -I'/home/biocbuild/bbs-3.17-bioc/R/library/RcppProgress/include' -I/usr/local/include -fopenmp -DSPLICEWIZ -fPIC -g -O2 -Wall -c synthReadGenerator.cpp -o synthReadGenerator.o g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.17-bioc/R/lib -L/usr/local/lib -o SpliceWiz.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -fopenmp -DSPLICEWIZ -L/home/biocbuild/bbs-3.17-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.17-bioc/R/library/00LOCK-SpliceWiz/00new/SpliceWiz/libs ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SpliceWiz)
SpliceWiz.Rcheck/tests/testthat.Rout.fail
R Under development (unstable) (2023-01-14 r83615) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 2 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Feb 22 13:41:46 Converting FASTA to local TwoBitFile...done
Feb 22 13:41:47 Connecting to genome TwoBitFile...done
Feb 22 13:41:47 Making local copy of GTF file...done
Feb 22 13:41:47 Extracting temp genome FASTA from TwoBit file
Feb 22 13:41:48 Generating synthetic reads, saving to /tmp/RtmpDvAAvk/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Feb 22 13:41:48 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.13.2
//================================= setting ==================================\\
|| ||
|| Function : Read alignment + Junction detection (RNA-Seq) ||
|| Input file : Reads.fa ||
|| Output file : AlignedReads.bam (BAM) ||
|| Index name : reference_index ||
|| ||
|| ------------------------------------ ||
|| ||
|| Threads : 1 ||
|| Phred offset : 33 ||
|| Min votes : 1 / 14 ||
|| Max mismatches : 3 ||
|| Max indel length : 5 ||
|| Report multi-mapping reads : yes ||
|| Max alignments per multi-mapping read : 1 ||
|| Annotations : transcripts.gtf (GTF) ||
|| ||
\\============================================================================//
//=============== Running (22-Feb-2023 13:41:48, pid=2459532) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| Create the output BAM file. ||
|| Check the index. ||
Unable top open index './reference_index'. Please make sure that the correct prefix is specified and you have the permission to read these files. For example, if there are files '/opt/my_index.reads', '/opt/my_index.files' and etc, the index prefix should be specified as '/opt/my_index' without any suffix.
Feb 22 13:41:52 Reference generated without non-polyA reference
Feb 22 13:41:52 Reference generated without Mappability reference
Feb 22 13:41:52 Reference generated without Blacklist exclusion
Feb 22 13:41:52 Converting FASTA to local TwoBitFile...done
Feb 22 13:41:54 Connecting to genome TwoBitFile...done
Feb 22 13:41:54 Making local copy of GTF file...done
Feb 22 13:41:54 Reading source GTF file...done
Feb 22 13:41:54 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Feb 22 13:41:58 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Feb 22 13:42:03 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Feb 22 13:42:11 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
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done
Feb 22 13:42:13 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Feb 22 13:42:15 Splice Annotations Filtered
Feb 22 13:42:16 Translating Alternate Splice Peptides...done
Feb 22 13:42:17 Splice Annotations finished
Reference build finished
Feb 22 13:42:18 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/RtmpDvAAvk/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/tmp/RtmpDvAAvk/02H003.bam processed (530 milliseconds)
Feb 22 13:42:18 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/RtmpDvAAvk/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Compiling data from threads
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/tmp/RtmpDvAAvk/02H003.bam processed (317 milliseconds)
Feb 22 13:42:19 SpliceWiz reference already exists in given directory
Feb 22 13:42:19 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmpDvAAvk/02H003.bam processed (520 milliseconds)
/tmp/RtmpDvAAvk/02H025.bam processed (411 milliseconds)
/tmp/RtmpDvAAvk/02H026.bam processed (641 milliseconds)
/tmp/RtmpDvAAvk/02H033.bam processed (636 milliseconds)
/tmp/RtmpDvAAvk/02H043.bam processed (395 milliseconds)
/tmp/RtmpDvAAvk/02H046.bam processed (589 milliseconds)
Feb 22 13:42:23 Using MulticoreParam 1 threads
Feb 22 13:42:23 Validating Experiment; checking COV files...
Feb 22 13:42:23 Compiling Sample Stats
Feb 22 13:42:23 Compiling Junction List...merging...done
Feb 22 13:42:25 Compiling Junction Stats...merging...done
Feb 22 13:42:33 Compiling Intron Retention List...done
Feb 22 13:42:34 Compiling Tandem Junction List...merging...done
Feb 22 13:42:36 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Feb 22 13:42:39 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Feb 22 13:42:52 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Feb 22 13:43:00 Generating NxtSE assays
Feb 22 13:43:01 Using MulticoreParam 1 threads
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Feb 22 13:43:18 Saving assays into H5 file
Feb 22 13:43:20 Saving auxiliary data
Feb 22 13:43:20 Assembling final NxtSE object
Feb 22 13:43:21 Saving final NxtSE object
Feb 22 13:43:21 SpliceWiz (NxtSE) Collation Finished
Feb 22 13:43:21 Loading NxtSE object from file...done
Feb 22 13:43:21 Removing overlapping introns...
Feb 22 13:43:21 Iterating through IR events to determine introns of main isoforms
Feb 22 13:43:22 Iteration 1
Feb 22 13:43:24 Iteration 2
Feb 22 13:43:27 SpliceWiz reference already exists in given directory
Feb 22 13:43:27 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmpDvAAvk/02H003.bam processed (548 milliseconds)
/tmp/RtmpDvAAvk/02H025.bam processed (428 milliseconds)
/tmp/RtmpDvAAvk/02H026.bam processed (673 milliseconds)
/tmp/RtmpDvAAvk/02H033.bam processed (672 milliseconds)
/tmp/RtmpDvAAvk/02H043.bam processed (413 milliseconds)
/tmp/RtmpDvAAvk/02H046.bam processed (611 milliseconds)
Feb 22 13:43:31 Using MulticoreParam 1 threads
Feb 22 13:43:31 Validating Experiment; checking COV files...
Feb 22 13:43:31 Compiling Sample Stats
Feb 22 13:43:31 Compiling Junction List...merging...done
Feb 22 13:43:33 Compiling Junction Stats...merging...done
Feb 22 13:43:41 Compiling Intron Retention List...done
Feb 22 13:43:43 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Feb 22 13:43:53 Generating NxtSE assays
Feb 22 13:43:55 Using MulticoreParam 1 threads
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Feb 22 13:44:12 Saving assays into H5 file
Feb 22 13:44:13 Saving auxiliary data
Feb 22 13:44:13 Assembling final NxtSE object
Feb 22 13:44:14 Saving final NxtSE object
Feb 22 13:44:14 SpliceWiz (NxtSE) Collation Finished
Feb 22 13:44:14 Loading NxtSE object from file...done
Feb 22 13:44:14 Removing overlapping introns...
Feb 22 13:44:14 Iterating through IR events to determine introns of main isoforms
Feb 22 13:44:16 Iteration 1
Feb 22 13:44:17 Iteration 2
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test-Mappa.R:20'): SpliceWiz pipeline reproduces NxtSE object ───────
Error in `.stop_quietly()`:
Backtrace:
▆
1. └─Rsubread::subjunc(...) at test-Mappa.R:20:4
2. └─Rsubread:::.load.delete.summary(output_file[i])
3. └─Rsubread:::.stop_quietly()
[ FAIL 1 | WARN 0 | SKIP 0 | PASS 28 ]
Error: Test failures
Execution halted
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 10.503 | 0.132 | 10.637 | |
| ASE-methods | 70.076 | 0.526 | 70.601 | |
| ASEFilter-class | 0.059 | 0.004 | 0.063 | |
| Build-Reference-methods | 24.294 | 0.172 | 24.468 | |
| Coverage | 1.206 | 0.008 | 1.212 | |
| Graphics-User-Interface | 0.000 | 0.000 | 0.001 | |
| Mappability-methods | 2.397 | 0.020 | 2.417 | |
| NxtSE-class | 54.962 | 0.622 | 55.671 | |
| Run_SpliceWiz_Filters | 7.562 | 0.016 | 7.579 | |
| STAR-methods | 0.006 | 0.000 | 0.004 | |
| View-Reference-methods | 0.004 | 0.004 | 0.008 | |
| collateData | 1.247 | 0.007 | 1.249 | |
| coord2GR | 0.021 | 0.000 | 0.021 | |
| example-SpliceWiz-data | 0.009 | 0.000 | 0.009 | |
| findSamples | 0.002 | 0.004 | 0.006 | |
| isCOV | 0.008 | 0.000 | 0.017 | |
| makeSE | 6.859 | 0.031 | 6.886 | |
| make_plot_data | 4.668 | 0.008 | 4.677 | |
| plotCoverage | 11.309 | 0.139 | 11.425 | |
| processBAM | 2.891 | 0.245 | 1.941 | |
| setSWthreads | 0.004 | 0.001 | 0.004 | |
| theme_white | 0.181 | 0.011 | 0.192 | |