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This page was generated on 2025-10-20 12:05 -0400 (Mon, 20 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 2097/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpliceWiz 1.11.0  (landing page)
Alex Chit Hei Wong
Snapshot Date: 2025-10-19 13:45 -0400 (Sun, 19 Oct 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)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    WARNINGS  


CHECK results for SpliceWiz on lconway

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.

raw results


Summary

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: 2025-10-20 01:59:02 -0400 (Mon, 20 Oct 2025)
EndedAt: 2025-10-20 02:22:55 -0400 (Mon, 20 Oct 2025)
EllapsedTime: 1433.1 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SpliceWiz.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.5.1 Patched (2025-09-10 r88807)
* 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 ... 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-3.22-bioc/meat/SpliceWiz.Rcheck/00install.out’ for details.
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.1.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 57.864  1.996  61.540
NxtSE-class             57.338  1.453  59.379
ASE-methods             31.225  0.483  32.617
covPlotObject-class     28.053  0.553  28.793
plotCoverage            19.209  0.185  19.484
Run_SpliceWiz_Filters    7.931  0.045   8.016
processBAM               4.142  1.010   3.569
* 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-3.22-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.


Installation output

SpliceWiz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceWiz
###
##############################################################################
##############################################################################


* 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: ‘MacOSX11.3.1.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
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)

Tests output

SpliceWiz.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-09-10 r88807) -- "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
Oct 20 02:09:53 Converting FASTA to local TwoBitFile...done
Oct 20 02:09:54 Connecting to genome TwoBitFile...done
Oct 20 02:09:54 Making local copy of GTF file...done
Oct 20 02:09:55 Extracting temp genome FASTA from TwoBit file
Oct 20 02:09:56 Generating synthetic reads, saving to /private/tmp/RtmpAenR1i/refWithMapExcl/Mappability/Reads.fa
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Oct 20 02:09:56 Cleaning temp genome / gene annotation files

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.23.8

//================================= setting ==================================\\
||                                                                            ||
||                Index name : reference_index                                ||
||               Index space : base space                                     ||
||               Index split : no-split                                       ||
||          Repeat threshold : 100 repeats                                    ||
||              Gapped index : no                                             ||
||                                                                            ||
||       Free / total memory : 44.7GB / 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=36.3k bps/s                                  ||
||   16%,   0 mins elapsed, rate=71.6k bps/s                                  ||
||   24%,   0 mins elapsed, rate=105.9k bps/s                                 ||
||   33%,   0 mins elapsed, rate=139.2k bps/s                                 ||
||   41%,   0 mins elapsed, rate=171.5k bps/s                                 ||
||   49%,   0 mins elapsed, rate=203.2k bps/s                                 ||
||   58%,   0 mins elapsed, rate=234.0k bps/s                                 ||
||   66%,   0 mins elapsed, rate=264.1k bps/s                                 ||
||   74%,   0 mins elapsed, rate=294.0k bps/s                                 ||
||   83%,   0 mins elapsed, rate=323.8k bps/s                                 ||
||   91%,   0 mins elapsed, rate=352.8k bps/s                                 ||
|| 3.0 GB of memory is needed for index building.                             ||
|| Build the index...                                                         ||
||    8%,   0 mins elapsed, rate=4.0k bps/s                                   ||
||   16%,   0 mins elapsed, rate=8.0k bps/s                                   ||
||   24%,   0 mins elapsed, rate=11.9k bps/s                                  ||
||   33%,   0 mins elapsed, rate=15.9k bps/s                                  ||
||   41%,   0 mins elapsed, rate=19.8k bps/s                                  ||
||   49%,   0 mins elapsed, rate=23.8k bps/s                                  ||
||   58%,   0 mins elapsed, rate=27.7k bps/s                                  ||
||   66%,   0 mins elapsed, rate=31.5k bps/s                                  ||
||   74%,   0 mins elapsed, rate=35.4k bps/s                                  ||
||   83%,   0 mins elapsed, rate=39.3k bps/s                                  ||
||   91%,   0 mins elapsed, rate=43.1k 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: 0.4 minutes.                      ||
||              Index ./reference_index was successfully built.               ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.23.8

//================================= 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 (20-Oct-2025 02:10:21, pid=1496) =================\\
||                                                                            ||
|| 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, 8.3 mins elapsed, rate=22.9k reads per second             ||
||   83% completed, 8.3 mins elapsed, rate=0.0k reads per second              ||
||   99% completed, 8.3 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 : 8.3 minutes                                  ||
||                                                                            ||
\\============================================================================//

Oct 20 02:18:42 Calculating Mappability Exclusion regions from: /tmp/RtmpAenR1i/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmpAenR1i/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 20 02:18:47 Reference generated without non-polyA reference
Oct 20 02:18:47 Reference generated without Mappability reference
Oct 20 02:18:47 Reference generated without Blacklist exclusion
Oct 20 02:18:47 Converting FASTA to local TwoBitFile...done
Oct 20 02:18:50 Connecting to genome TwoBitFile...done
Oct 20 02:18:50 Making local copy of GTF file...done
Oct 20 02:18:50 Reading source GTF file...done
Oct 20 02:18:51 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 20 02:18:52 Gene ontology not prepared for this reference
Oct 20 02:18:54 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Oct 20 02:18:58 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 20 02:19:05 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
done
Oct 20 02:19:08 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
Oct 20 02:19:09 Splice Annotations Filtered
Oct 20 02:19:10 Translating Alternate Splice Peptides...done
Oct 20 02:19:11 Splice Annotations finished

Reference build finished
Oct 20 02:19:12 Running SpliceWiz processBAM
Oct 20 02:19:13 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/RtmpAenR1i/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/RtmpAenR1i/02H003.bam processed (423 milliseconds)
Oct 20 02:19:13 SpliceWiz processBAM processed RtmpAenR1i/02H003.bam
Oct 20 02:19:13 Running SpliceWiz processBAM
Oct 20 02:19:15 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmpAenR1i/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/RtmpAenR1i/02H003.bam processed (423 milliseconds)
Oct 20 02:19:15 SpliceWiz processBAM processed RtmpAenR1i/02H003.bam
Oct 20 02:19:15 Reference generated without non-polyA reference
Oct 20 02:19:15 Reference generated without Mappability reference
Oct 20 02:19:15 Reference generated without Blacklist exclusion
Oct 20 02:19:15 Converting FASTA to local TwoBitFile...done
Oct 20 02:19:16 Connecting to genome TwoBitFile...done
Oct 20 02:19:16 Making local copy of GTF file...done
Oct 20 02:19:17 Reading source GTF file...done
Oct 20 02:19:17 Processing gtf file...
...genes
...transcripts
...CDS
Oct 20 02:19:17 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 20 02:19:18 Gene ontology not prepared for this reference
Oct 20 02:19:20 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Oct 20 02:19:24 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 20 02:19:31 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 20 02:19:32 Splice Annotations Filtered
Reference build finished
Oct 20 02:19:34 Running SpliceWiz processBAM
Oct 20 02:19:36 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H003.bam processed (440 milliseconds)
Oct 20 02:19:36 SpliceWiz processBAM processed RtmpAenR1i/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H025.bam processed (342 milliseconds)
Oct 20 02:19:36 SpliceWiz processBAM processed RtmpAenR1i/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H026.bam processed (511 milliseconds)
Oct 20 02:19:37 SpliceWiz processBAM processed RtmpAenR1i/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H033.bam processed (531 milliseconds)
Oct 20 02:19:38 SpliceWiz processBAM processed RtmpAenR1i/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H043.bam processed (418 milliseconds)
Oct 20 02:19:38 SpliceWiz processBAM processed RtmpAenR1i/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H046.bam processed (490 milliseconds)
Oct 20 02:19:39 SpliceWiz processBAM processed RtmpAenR1i/02H046.bam
Oct 20 02:19:40 Using MulticoreParam 1 threads
Oct 20 02:19:40 Validating Experiment; checking COV files...
Oct 20 02:19:40 Compiling Sample Stats
Oct 20 02:19:40 Compiling Junction List...merging...done
Oct 20 02:19:41 Compiling Junction Stats...merging...done
Oct 20 02:19:49 Compiling Intron Retention List...done
Oct 20 02:19:50 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 20 02:20:01 Generating NxtSE assays
Oct 20 02:20:02 Using MulticoreParam 1 threads

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Oct 20 02:20:18 Building Final NxtSE Object
Oct 20 02:20:18 ...consolidating assays to H5 file
Oct 20 02:20:19 ...packaging reference
Oct 20 02:20:19 ...synthesising NxtSE
Oct 20 02:20:19 ...determining how overlapping introns should be removed
Oct 20 02:20:22 SpliceWiz (NxtSE) Collation Finished
Oct 20 02:20:23 Loading NxtSE object from file...
Oct 20 02:20:23 ...loading reference (NxtSE)
Oct 20 02:20:23 ...linking assays
Oct 20 02:20:23 ...linking COV files
Oct 20 02:20:23 ...loading rowData
Oct 20 02:20:23 ...removing overlapping introns...
Oct 20 02:20:23 NxtSE loaded
Oct 20 02:20:23 SpliceWiz reference already exists in given directory
Oct 20 02:20:23 Running SpliceWiz processBAM
Oct 20 02:20:24 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H003.bam processed (413 milliseconds)
Oct 20 02:20:25 SpliceWiz processBAM processed RtmpAenR1i/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpAenR1i/02H025.bam processed (302 milliseconds)
Oct 20 02:20:25 SpliceWiz processBAM processed RtmpAenR1i/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H026.bam processed (489 milliseconds)
Oct 20 02:20:26 SpliceWiz processBAM processed RtmpAenR1i/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H033.bam processed (522 milliseconds)
Oct 20 02:20:26 SpliceWiz processBAM processed RtmpAenR1i/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H043.bam processed (321 milliseconds)
Oct 20 02:20:27 SpliceWiz processBAM processed RtmpAenR1i/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H046.bam processed (479 milliseconds)
Oct 20 02:20:27 SpliceWiz processBAM processed RtmpAenR1i/02H046.bam
Oct 20 02:20:28 Using MulticoreParam 1 threads
Oct 20 02:20:28 Validating Experiment; checking COV files...
Oct 20 02:20:28 Compiling Sample Stats
Oct 20 02:20:28 Compiling Junction List...merging...done
Oct 20 02:20:29 Compiling Junction Stats...merging...done
Oct 20 02:20:37 Compiling Intron Retention List...done
Oct 20 02:20:39 Compiling Tandem Junction List...merging...done
Oct 20 02:20:40 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Oct 20 02:20:43 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 20 02:20:54 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Oct 20 02:21:03 Generating NxtSE assays
Oct 20 02:21:04 Using MulticoreParam 1 threads

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  |=======================                                               |  33%
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  |======================================================================| 100%

Oct 20 02:21:20 Building Final NxtSE Object
Oct 20 02:21:20 ...consolidating assays to H5 file
Oct 20 02:21:22 ...packaging reference
Oct 20 02:21:22 ...synthesising NxtSE
Oct 20 02:21:22 ...determining how overlapping introns should be removed
Oct 20 02:21:25 SpliceWiz (NxtSE) Collation Finished
Oct 20 02:21:25 Loading NxtSE object from file...
Oct 20 02:21:25 ...loading reference (NxtSE)
Oct 20 02:21:25 ...linking assays
Oct 20 02:21:25 ...linking COV files
Oct 20 02:21:25 ...loading rowData
Oct 20 02:21:26 ...removing overlapping introns...
Oct 20 02:21:26 NxtSE loaded
Oct 20 02:21:26 SpliceWiz reference already exists in given directory
Oct 20 02:21:26 Running SpliceWiz processBAM
Oct 20 02:21:27 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H003.bam processed (418 milliseconds)
Oct 20 02:21:28 SpliceWiz processBAM processed RtmpAenR1i/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H025.bam processed (330 milliseconds)
Oct 20 02:21:28 SpliceWiz processBAM processed RtmpAenR1i/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H026.bam processed (510 milliseconds)
Oct 20 02:21:29 SpliceWiz processBAM processed RtmpAenR1i/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpAenR1i/02H033.bam processed (481 milliseconds)
Oct 20 02:21:29 SpliceWiz processBAM processed RtmpAenR1i/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H043.bam processed (326 milliseconds)
Oct 20 02:21:30 SpliceWiz processBAM processed RtmpAenR1i/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpAenR1i/02H046.bam processed (483 milliseconds)
Oct 20 02:21:30 SpliceWiz processBAM processed RtmpAenR1i/02H046.bam
Oct 20 02:21:31 Using MulticoreParam 1 threads
Oct 20 02:21:31 Validating Experiment; checking COV files...
Oct 20 02:21:31 Compiling Sample Stats
Oct 20 02:21:31 Compiling Junction List...merging...done
Oct 20 02:21:33 Compiling Junction Stats...merging...done
Oct 20 02:21:40 Compiling Intron Retention List...done
Oct 20 02:21:42 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 20 02:21:53 Generating NxtSE assays
Oct 20 02:21:54 Using MulticoreParam 1 threads

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Oct 20 02:22:09 Building Final NxtSE Object
Oct 20 02:22:09 ...consolidating assays to H5 file
Oct 20 02:22:11 ...packaging reference
Oct 20 02:22:11 ...synthesising NxtSE
Oct 20 02:22:11 ...determining how overlapping introns should be removed
Oct 20 02:22:14 SpliceWiz (NxtSE) Collation Finished
Oct 20 02:22:14 Loading NxtSE object from file...
Oct 20 02:22:14 ...loading reference (NxtSE)
Oct 20 02:22:14 ...linking assays
Oct 20 02:22:14 ...linking COV files
Oct 20 02:22:14 ...loading rowData
Oct 20 02:22:14 ...removing overlapping introns...
Oct 20 02:22:14 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 20 02:22:17 Reference generated without non-polyA reference
Oct 20 02:22:17 Reference generated without Mappability reference
Oct 20 02:22:17 Reference generated without Blacklist exclusion
Oct 20 02:22:17 Converting FASTA to local TwoBitFile...done
Oct 20 02:22:19 Connecting to genome TwoBitFile...done
Oct 20 02:22:19 Making local copy of GTF file...done
Oct 20 02:22:19 Reading source GTF file...done
Oct 20 02:22:19 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 20 02:22:20 Gene ontology not prepared for this reference
Oct 20 02:22:22 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Oct 20 02:22:26 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 20 02:22:33 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
done
Oct 20 02:22:35 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 20 02:22:37 Splice Annotations Filtered
Oct 20 02:22:38 Translating Alternate Splice Peptides...done
Oct 20 02:22:38 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 
416.483 288.552 785.618 

Example timings

SpliceWiz.Rcheck/SpliceWiz-Ex.timings

nameusersystemelapsed
ASE-GLM-edgeR2.4790.0972.728
ASE-methods31.225 0.48332.617
ASEFilter-class0.0490.0060.058
Build-Reference-methods57.864 1.99661.540
Coverage1.1460.0381.197
Gene-ontology-methods2.4720.1202.625
Graphics-User-Interface000
Mappability-methods2.5830.0772.679
NxtSE-class57.338 1.45359.379
Run_SpliceWiz_Filters7.9310.0458.016
STAR-methods0.0040.0090.030
View-Reference-methods0.2200.0440.285
collateData2.8920.0863.023
coord2GR0.0270.0020.030
covDataObject-class2.2160.0432.287
covPlotObject-class28.053 0.55328.793
covPlotly-class1.2980.0261.339
example-SpliceWiz-data0.0130.0020.016
findSamples0.0060.0040.012
isCOV0.0160.0050.021
makeSE2.1460.2002.399
make_plot_data0.0640.0030.067
plotCoverage19.209 0.18519.484
processBAM4.1421.0103.569
setSWthreads0.0040.0240.043
theme_white0.2450.0890.337