Alex Chit Hei Wong
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/SpliceWiz |
| git_branch: RELEASE_3_21 |
| git_last_commit: 2568ef4 |
| git_last_commit_date: 2025-05-08 12:30:24 -0400 (Thu, 08 May 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:40 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 | ||||
| Package 2081/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.10.1 (landing page) Alex Chit Hei Wong
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | WARNINGS | ||||||||||
|
To the developers/maintainers of the SpliceWiz package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SpliceWiz |
| Version: 1.10.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.10.1.tar.gz |
| StartedAt: 2025-10-15 14:00:20 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 14:23:36 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 1395.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 1 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.10.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.5.1 Patched (2025-06-14 r88325)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 16.0.0 (clang-1600.0.26.6)
GNU Fortran (GCC) 14.2.0
* running under: macOS Ventura 13.7.5
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.10.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 44 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ... WARNING
Found the following significant warnings:
Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/SpliceWiz.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code 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 whether startup messages can be suppressed ... 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'ASE-methods.Rd':
‘[limma:toptable]{limma::topTable}’
See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
NxtSE-class.Rd: SummarizedExperiment-class
SpliceWiz-package.Rd: SummarizedExperiment-class, rowData, colData
makeSE.Rd: colData
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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
NxtSE-class 69.671 1.016 71.029
Build-Reference-methods 67.326 1.637 71.898
ASE-methods 35.778 0.410 36.358
covPlotObject-class 25.025 0.561 25.621
plotCoverage 16.925 0.174 17.148
Run_SpliceWiz_Filters 10.063 0.037 10.164
processBAM 5.123 0.846 4.176
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 WARNING, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.21-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
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###
### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceWiz
###
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##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library’
* installing *source* package ‘SpliceWiz’ ...
** this is package ‘SpliceWiz’ version ‘1.10.1’
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FastaReader.cpp -o FastaReader.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c GZTools.cpp -o GZTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
ReadBlockProcessor_CoverageBlocks.cpp:251:16: warning: variable 'len' set but not used [-Wunused-but-set-variable]
unsigned int len=0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c covTools.cpp -o covTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c swEngine.cpp -o swEngine.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c synthReadGenerator.cpp -o synthReadGenerator.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -DSPLICEWIZ -F/Library/Frameworks/R.framework/.. -framework R
installing to /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/00LOCK-SpliceWiz/00new/SpliceWiz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the SpliceWiz package.
Please report the issue at <https://support.bioconductor.org/>.
** 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
R version 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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
Oct 15 14:11:47 Converting FASTA to local TwoBitFile...done
Oct 15 14:11:48 Connecting to genome TwoBitFile...done
Oct 15 14:11:48 Making local copy of GTF file...done
Oct 15 14:11:48 Extracting temp genome FASTA from TwoBit file
Oct 15 14:11:50 Generating synthetic reads, saving to /private/tmp/RtmpPtz5ps/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Oct 15 14:11:50 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.22.1
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 34.0GB / 64.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o genome.fa ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| No format issues were found ||
|| Scan uninformative subreads in reference sequences ... ||
|| Estimate the index size... ||
|| 8%, 0 mins elapsed, rate=81.2k bps/s ||
|| 16%, 0 mins elapsed, rate=141.7k bps/s ||
|| 24%, 0 mins elapsed, rate=196.3k bps/s ||
|| 33%, 0 mins elapsed, rate=249.0k bps/s ||
|| 41%, 0 mins elapsed, rate=299.7k bps/s ||
|| 49%, 0 mins elapsed, rate=349.5k bps/s ||
|| 58%, 0 mins elapsed, rate=397.2k bps/s ||
|| 66%, 0 mins elapsed, rate=443.4k bps/s ||
|| 74%, 0 mins elapsed, rate=489.5k bps/s ||
|| 83%, 0 mins elapsed, rate=534.6k bps/s ||
|| 91%, 0 mins elapsed, rate=577.8k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=5.5k bps/s ||
|| 16%, 0 mins elapsed, rate=11.0k bps/s ||
|| 24%, 0 mins elapsed, rate=16.4k bps/s ||
|| 33%, 0 mins elapsed, rate=21.8k bps/s ||
|| 41%, 0 mins elapsed, rate=27.2k bps/s ||
|| 49%, 0 mins elapsed, rate=32.5k bps/s ||
|| 58%, 0 mins elapsed, rate=37.7k bps/s ||
|| 66%, 0 mins elapsed, rate=42.9k bps/s ||
|| 74%, 0 mins elapsed, rate=48.1k bps/s ||
|| 83%, 0 mins elapsed, rate=53.3k bps/s ||
|| 91%, 0 mins elapsed, rate=58.4k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.3 minutes. ||
|| Index ./reference_index was successfully built. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.22.1
//================================= 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 (15-Oct-2025 14:12:09, pid=60324) =================\\
|| ||
|| 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. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 538 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 65% completed, 6.3 mins elapsed, rate=8.2k reads per second ||
|| 83% completed, 6.3 mins elapsed, rate=0.0k reads per second ||
|| 99% completed, 6.3 mins elapsed, rate=0.0k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 10,145 ||
|| Mapped : 10,145 (100.0%) ||
|| Uniquely mapped : 10,145 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 0 ||
|| ||
|| Junctions : 0 ||
|| Indels : 1 ||
|| ||
|| Running time : 6.3 minutes ||
|| ||
\\============================================================================//
Oct 15 14:18:26 Calculating Mappability Exclusion regions from: /tmp/RtmpPtz5ps/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmpPtz5ps/refWithMapExcl/Mappability/AlignedReads.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing Mappability Exclusions
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
SpliceWiz was compiled without OpenMP
Oct 15 14:18:30 Reference generated without non-polyA reference
Oct 15 14:18:30 Reference generated without Mappability reference
Oct 15 14:18:30 Reference generated without Blacklist exclusion
Oct 15 14:18:30 Converting FASTA to local TwoBitFile...done
Oct 15 14:18:31 Connecting to genome TwoBitFile...done
Oct 15 14:18:31 Making local copy of GTF file...done
Oct 15 14:18:31 Reading source GTF file...done
Oct 15 14:18:32 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 15 14:18:33 Gene ontology not prepared for this reference
Oct 15 14:18:36 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Oct 15 14:18:41 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
Oct 15 14:18:50 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Oct 15 14:18:53 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
Oct 15 14:18:55 Splice Annotations Filtered
Oct 15 14:18:57 Translating Alternate Splice Peptides...done
Oct 15 14:18:57 Splice Annotations finished
Reference build finished
Oct 15 14:18:58 Running SpliceWiz processBAM
Oct 15 14:19:00 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/RtmpPtz5ps/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/private/tmp/RtmpPtz5ps/02H003.bam processed (512 milliseconds)
Oct 15 14:19:00 SpliceWiz processBAM processed RtmpPtz5ps/02H003.bam
Oct 15 14:19:00 Running SpliceWiz processBAM
Oct 15 14:19:02 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/RtmpPtz5ps/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/private/tmp/RtmpPtz5ps/02H003.bam processed (600 milliseconds)
Oct 15 14:19:03 SpliceWiz processBAM processed RtmpPtz5ps/02H003.bam
Oct 15 14:19:03 Reference generated without non-polyA reference
Oct 15 14:19:03 Reference generated without Mappability reference
Oct 15 14:19:03 Reference generated without Blacklist exclusion
Oct 15 14:19:03 Converting FASTA to local TwoBitFile...done
Oct 15 14:19:05 Connecting to genome TwoBitFile...done
Oct 15 14:19:05 Making local copy of GTF file...done
Oct 15 14:19:05 Reading source GTF file...done
Oct 15 14:19:05 Processing gtf file...
...genes
...transcripts
...CDS
Oct 15 14:19:05 No protein information detected in reference! For full functionality, ensure there are valid entries with type == `CDS` in the gtf file. Protein reference and NMD annotation is skipped.
...exons
done
Oct 15 14:19:06 Gene ontology not prepared for this reference
Oct 15 14:19:09 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Oct 15 14:19:14 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
Oct 15 14:19:23 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
Oct 15 14:19:24 Splice Annotations Filtered
Reference build finished
Oct 15 14:19:27 Running SpliceWiz processBAM
Oct 15 14:19:29 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H003.bam processed (594 milliseconds)
Oct 15 14:19:30 SpliceWiz processBAM processed RtmpPtz5ps/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H025.bam processed (480 milliseconds)
Oct 15 14:19:30 SpliceWiz processBAM processed RtmpPtz5ps/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H026.bam processed (695 milliseconds)
Oct 15 14:19:31 SpliceWiz processBAM processed RtmpPtz5ps/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H033.bam processed (723 milliseconds)
Oct 15 14:19:32 SpliceWiz processBAM processed RtmpPtz5ps/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H043.bam processed (461 milliseconds)
Oct 15 14:19:32 SpliceWiz processBAM processed RtmpPtz5ps/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H046.bam processed (633 milliseconds)
Oct 15 14:19:33 SpliceWiz processBAM processed RtmpPtz5ps/02H046.bam
Oct 15 14:19:34 Using MulticoreParam 1 threads
Oct 15 14:19:34 Validating Experiment; checking COV files...
Oct 15 14:19:34 Compiling Sample Stats
Oct 15 14:19:34 Compiling Junction List...merging...done
Oct 15 14:19:36 Compiling Junction Stats...merging...done
Oct 15 14:19:46 Compiling Intron Retention List...done
Oct 15 14:19:48 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Oct 15 14:20:03 Generating NxtSE assays
Oct 15 14:20:04 Using MulticoreParam 1 threads
|
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|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Oct 15 14:20:24 Building Final NxtSE Object
Oct 15 14:20:24 ...consolidating assays to H5 file
Oct 15 14:20:26 ...packaging reference
Oct 15 14:20:26 ...synthesising NxtSE
Oct 15 14:20:26 ...determining how overlapping introns should be removed
Oct 15 14:20:30 SpliceWiz (NxtSE) Collation Finished
Oct 15 14:20:30 Loading NxtSE object from file...
Oct 15 14:20:30 ...loading reference (NxtSE)
Oct 15 14:20:30 ...linking assays
Oct 15 14:20:30 ...linking COV files
Oct 15 14:20:30 ...loading rowData
Oct 15 14:20:30 ...removing overlapping introns...
Oct 15 14:20:30 NxtSE loaded
Oct 15 14:20:30 SpliceWiz reference already exists in given directory
Oct 15 14:20:30 Running SpliceWiz processBAM
Oct 15 14:20:32 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H003.bam processed (570 milliseconds)
Oct 15 14:20:32 SpliceWiz processBAM processed RtmpPtz5ps/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H025.bam processed (458 milliseconds)
Oct 15 14:20:33 SpliceWiz processBAM processed RtmpPtz5ps/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H026.bam processed (499 milliseconds)
Oct 15 14:20:33 SpliceWiz processBAM processed RtmpPtz5ps/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpPtz5ps/02H033.bam processed (415 milliseconds)
Oct 15 14:20:34 SpliceWiz processBAM processed RtmpPtz5ps/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H043.bam processed (426 milliseconds)
Oct 15 14:20:34 SpliceWiz processBAM processed RtmpPtz5ps/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H046.bam processed (663 milliseconds)
Oct 15 14:20:35 SpliceWiz processBAM processed RtmpPtz5ps/02H046.bam
Oct 15 14:20:37 Using MulticoreParam 1 threads
Oct 15 14:20:37 Validating Experiment; checking COV files...
Oct 15 14:20:37 Compiling Sample Stats
Oct 15 14:20:37 Compiling Junction List...merging...done
Oct 15 14:20:38 Compiling Junction Stats...merging...done
Oct 15 14:20:48 Compiling Intron Retention List...done
Oct 15 14:20:50 Compiling Tandem Junction List...merging...done
Oct 15 14:20:51 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Oct 15 14:20:56 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Oct 15 14:21:09 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Oct 15 14:21:20 Generating NxtSE assays
Oct 15 14:21:21 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Oct 15 14:21:42 Building Final NxtSE Object
Oct 15 14:21:42 ...consolidating assays to H5 file
Oct 15 14:21:43 ...packaging reference
Oct 15 14:21:43 ...synthesising NxtSE
Oct 15 14:21:44 ...determining how overlapping introns should be removed
Oct 15 14:21:47 SpliceWiz (NxtSE) Collation Finished
Oct 15 14:21:47 Loading NxtSE object from file...
Oct 15 14:21:47 ...loading reference (NxtSE)
Oct 15 14:21:47 ...linking assays
Oct 15 14:21:47 ...linking COV files
Oct 15 14:21:47 ...loading rowData
Oct 15 14:21:47 ...removing overlapping introns...
Oct 15 14:21:47 NxtSE loaded
Oct 15 14:21:48 SpliceWiz reference already exists in given directory
Oct 15 14:21:48 Running SpliceWiz processBAM
Oct 15 14:21:49 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H003.bam processed (573 milliseconds)
Oct 15 14:21:50 SpliceWiz processBAM processed RtmpPtz5ps/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H025.bam processed (464 milliseconds)
Oct 15 14:21:50 SpliceWiz processBAM processed RtmpPtz5ps/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H026.bam processed (687 milliseconds)
Oct 15 14:21:51 SpliceWiz processBAM processed RtmpPtz5ps/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H033.bam processed (688 milliseconds)
Oct 15 14:21:52 SpliceWiz processBAM processed RtmpPtz5ps/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H043.bam processed (439 milliseconds)
Oct 15 14:21:52 SpliceWiz processBAM processed RtmpPtz5ps/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpPtz5ps/02H046.bam processed (633 milliseconds)
Oct 15 14:21:53 SpliceWiz processBAM processed RtmpPtz5ps/02H046.bam
Oct 15 14:21:54 Using MulticoreParam 1 threads
Oct 15 14:21:54 Validating Experiment; checking COV files...
Oct 15 14:21:54 Compiling Sample Stats
Oct 15 14:21:54 Compiling Junction List...merging...done
Oct 15 14:21:56 Compiling Junction Stats...merging...done
Oct 15 14:22:06 Compiling Intron Retention List...done
Oct 15 14:22:07 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Oct 15 14:22:21 Generating NxtSE assays
Oct 15 14:22:22 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Oct 15 14:22:42 Building Final NxtSE Object
Oct 15 14:22:42 ...consolidating assays to H5 file
Oct 15 14:22:44 ...packaging reference
Oct 15 14:22:44 ...synthesising NxtSE
Oct 15 14:22:44 ...determining how overlapping introns should be removed
Oct 15 14:22:48 SpliceWiz (NxtSE) Collation Finished
Oct 15 14:22:48 Loading NxtSE object from file...
Oct 15 14:22:48 ...loading reference (NxtSE)
Oct 15 14:22:48 ...linking assays
Oct 15 14:22:48 ...linking COV files
Oct 15 14:22:48 ...loading rowData
Oct 15 14:22:48 ...removing overlapping introns...
Oct 15 14:22:48 NxtSE loaded
path paired strand depth mean_frag_size
02H003 ../SpliceWiz_Output/02H003.txt.gz TRUE -1 106256 149.3108
02H025 ../SpliceWiz_Output/02H025.txt.gz TRUE -1 84872 151.5914
02H026 ../SpliceWiz_Output/02H026.txt.gz TRUE -1 131514 150.3238
02H033 ../SpliceWiz_Output/02H033.txt.gz TRUE -1 129013 153.9754
02H043 ../SpliceWiz_Output/02H043.txt.gz TRUE -1 80254 155.4004
02H046 ../SpliceWiz_Output/02H046.txt.gz TRUE -1 120174 151.2840
directionality_strength Intergenic_Fraction rRNA_Fraction
02H003 9850 0 0
02H025 9848 0 0
02H026 9848 0 0
02H033 9855 0 0
02H043 9841 0 0
02H046 9857 0 0
NonPolyA_Fraction Mitochondrial_Fraction Unanno_Jn_Fraction
02H003 0 0 0.013449472
02H025 0 0 0.011203515
02H026 0 0 0.007282382
02H033 0 0 0.006310241
02H043 0 0 0.005871040
02H046 0 0 0.009819533
NMD_Jn_Fraction Fraction_Splice_Reads Fraction_Span_Reads IRBurden_clean
02H003 0.019509970 0.3506908 0.1735243 0.05796583
02H025 0.019360162 0.3712414 0.1591691 0.03963531
02H026 0.004298323 0.3980261 0.1615037 0.02576549
02H033 0.007705562 0.4003550 0.1734089 0.03090263
02H043 0.028069104 0.3671219 0.1807511 0.03762138
02H046 0.010542303 0.3725598 0.1603508 0.05099352
IRBurden_exitrons IRBurden_clean_unstranded IRBurden_exitrons_unstranded
02H003 0.1291810 0.03844293 0.1296020
02H025 0.1192351 0.02730399 0.1194005
02H026 0.1231055 0.02010410 0.1231939
02H033 0.1378958 0.02300500 0.1380215
02H043 0.1392935 0.02286515 0.1397365
02H046 0.1132136 0.03359077 0.1133852
IRBurden_antisense
02H003 0.021393335
02H025 0.013191532
02H026 0.006007119
02H033 0.008453742
02H043 0.015837096
02H046 0.019043703
MD5 is fcdc53e0f7fbd843529077ebd26dd058
Oct 15 14:22:52 Reference generated without non-polyA reference
Oct 15 14:22:52 Reference generated without Mappability reference
Oct 15 14:22:52 Reference generated without Blacklist exclusion
Oct 15 14:22:52 Converting FASTA to local TwoBitFile...done
Oct 15 14:22:53 Connecting to genome TwoBitFile...done
Oct 15 14:22:53 Making local copy of GTF file...done
Oct 15 14:22:53 Reading source GTF file...done
Oct 15 14:22:54 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 15 14:22:55 Gene ontology not prepared for this reference
Oct 15 14:22:57 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Oct 15 14:23:02 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
Oct 15 14:23:11 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Oct 15 14:23:14 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
Oct 15 14:23:15 Splice Annotations Filtered
Oct 15 14:23:17 Translating Alternate Splice Peptides...done
Oct 15 14:23:17 Splice Annotations finished
Reference build finished
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
465.976 237.365 711.243
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 2.554 | 0.122 | 2.679 | |
| ASE-methods | 35.778 | 0.410 | 36.358 | |
| ASEFilter-class | 0.044 | 0.004 | 0.048 | |
| Build-Reference-methods | 67.326 | 1.637 | 71.898 | |
| Coverage | 1.095 | 0.041 | 1.165 | |
| Gene-ontology-methods | 2.493 | 0.175 | 2.690 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 3.394 | 0.058 | 3.479 | |
| NxtSE-class | 69.671 | 1.016 | 71.029 | |
| Run_SpliceWiz_Filters | 10.063 | 0.037 | 10.164 | |
| STAR-methods | 0.006 | 0.013 | 0.028 | |
| View-Reference-methods | 0.282 | 0.023 | 0.308 | |
| collateData | 3.415 | 0.065 | 3.490 | |
| coord2GR | 0.028 | 0.002 | 0.030 | |
| covDataObject-class | 1.881 | 0.023 | 1.911 | |
| covPlotObject-class | 25.025 | 0.561 | 25.621 | |
| covPlotly-class | 1.058 | 0.041 | 1.099 | |
| example-SpliceWiz-data | 0.019 | 0.003 | 0.023 | |
| findSamples | 0.007 | 0.006 | 0.012 | |
| isCOV | 0.019 | 0.005 | 0.025 | |
| makeSE | 2.203 | 0.110 | 2.319 | |
| make_plot_data | 0.048 | 0.003 | 0.050 | |
| plotCoverage | 16.925 | 0.174 | 17.148 | |
| processBAM | 5.123 | 0.846 | 4.176 | |
| setSWthreads | 0.005 | 0.012 | 0.020 | |
| theme_white | 0.218 | 0.073 | 0.293 | |