Alex Chit Hei Wong
| Snapshot Date: 2025-08-11 13:45 -0400 (Mon, 11 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/SpliceWiz |
| git_branch: devel |
| git_last_commit: ff5b222 |
| git_last_commit_date: 2025-04-15 12:53:12 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-08-12 12:10 -0400 (Tue, 12 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4818 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4553 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4595 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4537 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4535 |
| 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 2064/2317 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.11.0 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 24.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
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: 1.11.0 |
| 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_1.11.0.tar.gz |
| StartedAt: 2025-08-12 00:28:18 -0400 (Tue, 12 Aug 2025) |
| EndedAt: 2025-08-12 00:49:24 -0400 (Tue, 12 Aug 2025) |
| EllapsedTime: 1266.4 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 0 |
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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_1.11.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 14.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.11.0’
* 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 ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* 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
Build-Reference-methods 55.692 1.842 58.831
NxtSE-class 54.771 1.414 56.674
ASE-methods 31.308 0.250 31.727
covPlotObject-class 22.517 0.535 23.237
plotCoverage 16.201 0.227 16.535
Run_SpliceWiz_Filters 7.368 0.043 7.450
processBAM 4.066 0.995 3.531
* 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: 4 NOTEs
See
‘/Users/biocbuild/bbs-3.22-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceWiz
###
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##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘SpliceWiz’ ...
** this is package ‘SpliceWiz’ version ‘1.11.0’
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FastaReader.cpp -o FastaReader.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c GZTools.cpp -o GZTools.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c covTools.cpp -o covTools.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c swEngine.cpp -o swEngine.o
clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c synthReadGenerator.cpp -o synthReadGenerator.o
clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/Resources/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
R version 4.5.1 (2025-06-13) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-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 1 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Aug 12 00:38:32 Converting FASTA to local TwoBitFile...done
Aug 12 00:38:33 Connecting to genome TwoBitFile...done
Aug 12 00:38:33 Making local copy of GTF file...done
Aug 12 00:38:33 Extracting temp genome FASTA from TwoBit file
Aug 12 00:38:34 Generating synthetic reads, saving to /private/tmp/RtmpxgLzWx/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Aug 12 00:38:34 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.23.3
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 53.0GB / 96.0GB ||
|| ||
|| 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=39.9k bps/s ||
|| 16%, 0 mins elapsed, rate=78.6k bps/s ||
|| 24%, 0 mins elapsed, rate=116.3k bps/s ||
|| 33%, 0 mins elapsed, rate=152.9k bps/s ||
|| 41%, 0 mins elapsed, rate=188.8k bps/s ||
|| 49%, 0 mins elapsed, rate=224.0k bps/s ||
|| 58%, 0 mins elapsed, rate=258.5k bps/s ||
|| 66%, 0 mins elapsed, rate=292.4k bps/s ||
|| 74%, 0 mins elapsed, rate=325.8k bps/s ||
|| 83%, 0 mins elapsed, rate=358.5k bps/s ||
|| 91%, 0 mins elapsed, rate=389.9k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=4.4k bps/s ||
|| 16%, 0 mins elapsed, rate=8.7k bps/s ||
|| 24%, 0 mins elapsed, rate=13.1k bps/s ||
|| 33%, 0 mins elapsed, rate=17.4k bps/s ||
|| 41%, 0 mins elapsed, rate=21.7k bps/s ||
|| 49%, 0 mins elapsed, rate=26.0k bps/s ||
|| 58%, 0 mins elapsed, rate=30.3k bps/s ||
|| 66%, 0 mins elapsed, rate=34.5k bps/s ||
|| 74%, 0 mins elapsed, rate=38.8k bps/s ||
|| 83%, 0 mins elapsed, rate=43.0k bps/s ||
|| 91%, 0 mins elapsed, rate=47.2k 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 2.23.3
//================================= 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 (12-Aug-2025 00:38:54, pid=15213) =================\\
|| ||
|| 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, 6.5 mins elapsed, rate=24.9k reads per second ||
|| 83% completed, 6.5 mins elapsed, rate=0.0k reads per second ||
|| 99% completed, 6.5 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 : 6.5 minutes ||
|| ||
\\============================================================================//
Aug 12 00:45:22 Calculating Mappability Exclusion regions from: /tmp/RtmpxgLzWx/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmpxgLzWx/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
Aug 12 00:45:27 Reference generated without non-polyA reference
Aug 12 00:45:27 Reference generated without Mappability reference
Aug 12 00:45:27 Reference generated without Blacklist exclusion
Aug 12 00:45:27 Converting FASTA to local TwoBitFile...done
Aug 12 00:45:28 Connecting to genome TwoBitFile...done
Aug 12 00:45:28 Making local copy of GTF file...done
Aug 12 00:45:28 Reading source GTF file...done
Aug 12 00:45:28 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Aug 12 00:45:29 Gene ontology not prepared for this reference
Aug 12 00:45:32 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Aug 12 00:45:36 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
Aug 12 00:45:43 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Aug 12 00:45:46 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
Aug 12 00:45:47 Splice Annotations Filtered
Aug 12 00:45:48 Translating Alternate Splice Peptides...done
Aug 12 00:45:48 Splice Annotations finished
Reference build finished
Aug 12 00:45:50 Running SpliceWiz processBAM
Aug 12 00:45:51 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/RtmpxgLzWx/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/RtmpxgLzWx/02H003.bam processed (450 milliseconds)
Aug 12 00:45:51 SpliceWiz processBAM processed RtmpxgLzWx/02H003.bam
Aug 12 00:45:51 Running SpliceWiz processBAM
Aug 12 00:45:52 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmpxgLzWx/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/RtmpxgLzWx/02H003.bam processed (412 milliseconds)
Aug 12 00:45:53 SpliceWiz processBAM processed RtmpxgLzWx/02H003.bam
Aug 12 00:45:53 Reference generated without non-polyA reference
Aug 12 00:45:53 Reference generated without Mappability reference
Aug 12 00:45:53 Reference generated without Blacklist exclusion
Aug 12 00:45:53 Converting FASTA to local TwoBitFile...done
Aug 12 00:45:54 Connecting to genome TwoBitFile...done
Aug 12 00:45:54 Making local copy of GTF file...done
Aug 12 00:45:54 Reading source GTF file...done
Aug 12 00:45:54 Processing gtf file...
...genes
...transcripts
...CDS
Aug 12 00:45:55 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
Aug 12 00:45:55 Gene ontology not prepared for this reference
Aug 12 00:45:58 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Aug 12 00:46:01 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
Aug 12 00:46:08 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
Aug 12 00:46:09 Splice Annotations Filtered
Reference build finished
Aug 12 00:46:11 Running SpliceWiz processBAM
Aug 12 00:46:13 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H003.bam processed (390 milliseconds)
Aug 12 00:46:13 SpliceWiz processBAM processed RtmpxgLzWx/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H025.bam processed (350 milliseconds)
Aug 12 00:46:13 SpliceWiz processBAM processed RtmpxgLzWx/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H026.bam processed (512 milliseconds)
Aug 12 00:46:14 SpliceWiz processBAM processed RtmpxgLzWx/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H033.bam processed (489 milliseconds)
Aug 12 00:46:14 SpliceWiz processBAM processed RtmpxgLzWx/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H043.bam processed (302 milliseconds)
Aug 12 00:46:15 SpliceWiz processBAM processed RtmpxgLzWx/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpxgLzWx/02H046.bam processed (472 milliseconds)
Aug 12 00:46:15 SpliceWiz processBAM processed RtmpxgLzWx/02H046.bam
Aug 12 00:46:16 Using MulticoreParam 1 threads
Aug 12 00:46:16 Validating Experiment; checking COV files...
Aug 12 00:46:16 Compiling Sample Stats
Aug 12 00:46:16 Compiling Junction List...merging...done
Aug 12 00:46:18 Compiling Junction Stats...merging...done
Aug 12 00:46:24 Compiling Intron Retention List...done
Aug 12 00:46:26 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Aug 12 00:46:36 Generating NxtSE assays
Aug 12 00:46:37 Using MulticoreParam 1 threads
|
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|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Aug 12 00:46:52 Building Final NxtSE Object
Aug 12 00:46:52 ...consolidating assays to H5 file
Aug 12 00:46:53 ...packaging reference
Aug 12 00:46:54 ...synthesising NxtSE
Aug 12 00:46:54 ...determining how overlapping introns should be removed
Aug 12 00:46:57 SpliceWiz (NxtSE) Collation Finished
Aug 12 00:46:57 Loading NxtSE object from file...
Aug 12 00:46:57 ...loading reference (NxtSE)
Aug 12 00:46:57 ...linking assays
Aug 12 00:46:57 ...linking COV files
Aug 12 00:46:57 ...loading rowData
Aug 12 00:46:57 ...removing overlapping introns...
Aug 12 00:46:57 NxtSE loaded
Aug 12 00:46:58 SpliceWiz reference already exists in given directory
Aug 12 00:46:58 Running SpliceWiz processBAM
Aug 12 00:46:59 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpxgLzWx/02H003.bam processed (411 milliseconds)
Aug 12 00:46:59 SpliceWiz processBAM processed RtmpxgLzWx/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H025.bam processed (346 milliseconds)
Aug 12 00:46:59 SpliceWiz processBAM processed RtmpxgLzWx/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H026.bam processed (538 milliseconds)
Aug 12 00:47:00 SpliceWiz processBAM processed RtmpxgLzWx/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H033.bam processed (533 milliseconds)
Aug 12 00:47:01 SpliceWiz processBAM processed RtmpxgLzWx/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H043.bam processed (335 milliseconds)
Aug 12 00:47:01 SpliceWiz processBAM processed RtmpxgLzWx/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H046.bam processed (487 milliseconds)
Aug 12 00:47:01 SpliceWiz processBAM processed RtmpxgLzWx/02H046.bam
Aug 12 00:47:02 Using MulticoreParam 1 threads
Aug 12 00:47:02 Validating Experiment; checking COV files...
Aug 12 00:47:02 Compiling Sample Stats
Aug 12 00:47:03 Compiling Junction List...merging...done
Aug 12 00:47:04 Compiling Junction Stats...merging...done
Aug 12 00:47:11 Compiling Intron Retention List...done
Aug 12 00:47:12 Compiling Tandem Junction List...merging...done
Aug 12 00:47:13 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Aug 12 00:47:17 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Aug 12 00:47:27 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Aug 12 00:47:36 Generating NxtSE assays
Aug 12 00:47:37 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Aug 12 00:47:52 Building Final NxtSE Object
Aug 12 00:47:52 ...consolidating assays to H5 file
Aug 12 00:47:54 ...packaging reference
Aug 12 00:47:54 ...synthesising NxtSE
Aug 12 00:47:54 ...determining how overlapping introns should be removed
Aug 12 00:47:57 SpliceWiz (NxtSE) Collation Finished
Aug 12 00:47:57 Loading NxtSE object from file...
Aug 12 00:47:57 ...loading reference (NxtSE)
Aug 12 00:47:57 ...linking assays
Aug 12 00:47:57 ...linking COV files
Aug 12 00:47:57 ...loading rowData
Aug 12 00:47:57 ...removing overlapping introns...
Aug 12 00:47:57 NxtSE loaded
Aug 12 00:47:58 SpliceWiz reference already exists in given directory
Aug 12 00:47:58 Running SpliceWiz processBAM
Aug 12 00:47:59 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H003.bam processed (411 milliseconds)
Aug 12 00:47:59 SpliceWiz processBAM processed RtmpxgLzWx/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H025.bam processed (345 milliseconds)
Aug 12 00:47:59 SpliceWiz processBAM processed RtmpxgLzWx/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H026.bam processed (545 milliseconds)
Aug 12 00:48:00 SpliceWiz processBAM processed RtmpxgLzWx/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H033.bam processed (499 milliseconds)
Aug 12 00:48:01 SpliceWiz processBAM processed RtmpxgLzWx/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H043.bam processed (321 milliseconds)
Aug 12 00:48:01 SpliceWiz processBAM processed RtmpxgLzWx/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpxgLzWx/02H046.bam processed (464 milliseconds)
Aug 12 00:48:01 SpliceWiz processBAM processed RtmpxgLzWx/02H046.bam
Aug 12 00:48:03 Using MulticoreParam 1 threads
Aug 12 00:48:03 Validating Experiment; checking COV files...
Aug 12 00:48:03 Compiling Sample Stats
Aug 12 00:48:03 Compiling Junction List...merging...done
Aug 12 00:48:04 Compiling Junction Stats...merging...done
Aug 12 00:48:11 Compiling Intron Retention List...done
Aug 12 00:48:13 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Aug 12 00:48:24 Generating NxtSE assays
Aug 12 00:48:25 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Aug 12 00:48:40 Building Final NxtSE Object
Aug 12 00:48:40 ...consolidating assays to H5 file
Aug 12 00:48:41 ...packaging reference
Aug 12 00:48:41 ...synthesising NxtSE
Aug 12 00:48:42 ...determining how overlapping introns should be removed
Aug 12 00:48:44 SpliceWiz (NxtSE) Collation Finished
Aug 12 00:48:44 Loading NxtSE object from file...
Aug 12 00:48:44 ...loading reference (NxtSE)
Aug 12 00:48:45 ...linking assays
Aug 12 00:48:45 ...linking COV files
Aug 12 00:48:45 ...loading rowData
Aug 12 00:48:45 ...removing overlapping introns...
Aug 12 00:48:45 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
Aug 12 00:48:48 Reference generated without non-polyA reference
Aug 12 00:48:48 Reference generated without Mappability reference
Aug 12 00:48:48 Reference generated without Blacklist exclusion
Aug 12 00:48:48 Converting FASTA to local TwoBitFile...done
Aug 12 00:48:49 Connecting to genome TwoBitFile...done
Aug 12 00:48:49 Making local copy of GTF file...done
Aug 12 00:48:49 Reading source GTF file...done
Aug 12 00:48:49 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Aug 12 00:48:50 Gene ontology not prepared for this reference
Aug 12 00:48:53 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Aug 12 00:48:56 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
Aug 12 00:49:03 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Aug 12 00:49:06 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
Aug 12 00:49:07 Splice Annotations Filtered
Aug 12 00:49:08 Translating Alternate Splice Peptides...done
Aug 12 00:49:08 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
401.784 218.825 655.657
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 3.262 | 0.164 | 3.442 | |
| ASE-methods | 31.308 | 0.250 | 31.727 | |
| ASEFilter-class | 0.049 | 0.006 | 0.055 | |
| Build-Reference-methods | 55.692 | 1.842 | 58.831 | |
| Coverage | 0.901 | 0.033 | 0.939 | |
| Gene-ontology-methods | 2.129 | 0.127 | 2.275 | |
| Graphics-User-Interface | 0.001 | 0.000 | 0.000 | |
| Mappability-methods | 2.542 | 0.053 | 2.619 | |
| NxtSE-class | 54.771 | 1.414 | 56.674 | |
| Run_SpliceWiz_Filters | 7.368 | 0.043 | 7.450 | |
| STAR-methods | 0.005 | 0.013 | 0.045 | |
| View-Reference-methods | 0.221 | 0.029 | 0.258 | |
| collateData | 2.825 | 0.086 | 2.951 | |
| coord2GR | 0.031 | 0.003 | 0.034 | |
| covDataObject-class | 1.885 | 0.033 | 1.955 | |
| covPlotObject-class | 22.517 | 0.535 | 23.237 | |
| covPlotly-class | 1.366 | 0.022 | 1.402 | |
| example-SpliceWiz-data | 0.017 | 0.003 | 0.020 | |
| findSamples | 0.007 | 0.005 | 0.012 | |
| isCOV | 0.018 | 0.003 | 0.021 | |
| makeSE | 1.972 | 0.148 | 2.153 | |
| make_plot_data | 0.065 | 0.003 | 0.068 | |
| plotCoverage | 16.201 | 0.227 | 16.535 | |
| processBAM | 4.066 | 0.995 | 3.531 | |
| setSWthreads | 0.004 | 0.010 | 0.025 | |
| theme_white | 0.167 | 0.055 | 0.227 | |