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This page was generated on 2024-05-04 11:38:37 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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 2054/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpliceWiz 1.6.0  (landing page)
Alex Chit Hei Wong
Snapshot Date: 2024-05-03 14:00:19 -0400 (Fri, 03 May 2024)
git_url: https://git.bioconductor.org/packages/SpliceWiz
git_branch: RELEASE_3_19
git_last_commit: 0677691
git_last_commit_date: 2024-04-30 11:43:22 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    ERROR  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for SpliceWiz on palomino3


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: 1.6.0
Command: F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpliceWiz.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SpliceWiz_1.6.0.tar.gz
StartedAt: 2024-05-04 08:28:52 -0400 (Sat, 04 May 2024)
EndedAt: 2024-05-04 08:44:44 -0400 (Sat, 04 May 2024)
EllapsedTime: 952.0 seconds
RetCode: 0
Status:   OK  
CheckDir: SpliceWiz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpliceWiz.install-out.txt --library=F:\biocbuild\bbs-3.19-bioc\R\library --no-vignettes --timings SpliceWiz_1.6.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck'
* using R version 4.4.0 beta (2024-04-15 r86425 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'SpliceWiz/DESCRIPTION' ... OK
* this is package 'SpliceWiz' version '1.6.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'SpliceWiz' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
* 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 ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'F:/biocbuild/bbs-3.19-bioc/R/library/SpliceWiz/libs/x64/SpliceWiz.dll':
  Found '_assert', possibly from 'assert' (C)
  Found '_exit', possibly from '_exit' (C)
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
Build-Reference-methods 59.58   2.28   69.73
NxtSE-class             56.64   2.05   59.44
ASE-methods             31.98   0.22   32.24
covPlotObject-class     25.10   0.72   25.83
plotCoverage            15.21   0.31   15.55
Run_SpliceWiz_Filters    8.64   0.01    8.65
* 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: 3 NOTEs
See
  'F:/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck/00check.log'
for details.


Installation output

SpliceWiz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD INSTALL SpliceWiz
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.19-bioc/R/library'
* installing *source* package 'SpliceWiz' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++11
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c BAM2blocks.cpp -o BAM2blocks.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FastaReader.cpp -o FastaReader.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c FragmentBlocks.cpp -o FragmentBlocks.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c GZTools.cpp -o GZTools.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c covTools.cpp -o covTools.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c main.cpp -o main.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c swEngine.cpp -o swEngine.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.19-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.19-bioc/R/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -fopenmp -DSPLICEWIZ   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c synthReadGenerator.cpp -o synthReadGenerator.o
g++ -shared -s -static-libgcc -o SpliceWiz.dll tmp.def BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -fopenmp -DSPLICEWIZ -LF:/biocbuild/bbs-3.19-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.19-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.19-bioc/R/library/00LOCK-SpliceWiz/00new/SpliceWiz/libs/x64
** 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
** 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 4.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64

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
May 04 8:39:44 AM Converting FASTA to local TwoBitFile...done
May 04 8:39:46 AM Connecting to genome TwoBitFile...done
May 04 8:39:46 AM Making local copy of GTF file...done
May 04 8:39:47 AM Extracting temp genome FASTA from TwoBit file
May 04 8:39:48 AM Generating synthetic reads, saving to F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\refWithMapExcl/Mappability/Reads.fa
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
May 04 8:39:48 AM Cleaning temp genome / gene annotation files

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.18.0

//================================= setting ==================================\\
||                                                                            ||
||                Index name : reference_index                                ||
||               Index space : base space                                     ||
||               Index split : no-split                                       ||
||          Repeat threshold : 100 repeats                                    ||
||              Gapped index : no                                             ||
||                                                                            ||
||       Free / total memory : 42.0GB / 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=28.2k bps/s                                  ||
||   16%,   0 mins elapsed, rate=55.5k bps/s                                  ||
||   24%,   0 mins elapsed, rate=82.1k bps/s                                  ||
||   33%,   0 mins elapsed, rate=108.0k bps/s                                 ||
||   41%,   0 mins elapsed, rate=133.2k bps/s                                 ||
||   49%,   0 mins elapsed, rate=157.9k bps/s                                 ||
||   58%,   0 mins elapsed, rate=182.1k bps/s                                 ||
||   66%,   0 mins elapsed, rate=205.6k bps/s                                 ||
||   74%,   0 mins elapsed, rate=228.4k bps/s                                 ||
||   83%,   0 mins elapsed, rate=250.6k bps/s                                 ||
||   91%,   0 mins elapsed, rate=272.8k bps/s                                 ||
|| 3.0 GB of memory is needed for index building.                             ||
|| Build the index...                                                         ||
||    8%,   0 mins elapsed, rate=3.3k bps/s                                   ||
||   16%,   0 mins elapsed, rate=6.6k bps/s                                   ||
||   24%,   0 mins elapsed, rate=9.9k bps/s                                   ||
||   33%,   0 mins elapsed, rate=13.2k bps/s                                  ||
||   41%,   0 mins elapsed, rate=16.5k bps/s                                  ||
||   49%,   0 mins elapsed, rate=19.8k bps/s                                  ||
||   58%,   0 mins elapsed, rate=23.0k bps/s                                  ||
||   66%,   0 mins elapsed, rate=26.2k bps/s                                  ||
||   74%,   0 mins elapsed, rate=29.4k bps/s                                  ||
||   83%,   0 mins elapsed, rate=32.6k bps/s                                  ||
||   91%,   0 mins elapsed, rate=35.8k 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 F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\refWithMapExcl\refe ... ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.18.0

//================================= 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 (04-May-2024 08:40:05, pid=54564) =================\\
||                                                                            ||
|| 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, 0.5 mins elapsed, rate=34.2k reads per second             ||
||   83% completed, 0.6 mins elapsed, rate=0.3k reads per second              ||
||   99% completed, 0.6 mins elapsed, rate=0.3k reads per second              ||
||                                                                            ||
||                           Completed successfully.                          ||
||                                                                            ||
\\====================================    ====================================//

//================================   Summary =================================\\
||                                                                            ||
||                 Total reads : 10145                                        ||
||                      Mapped : 10145 (100.0%)                               ||
||             Uniquely mapped : 10145                                        ||
||               Multi-mapping : 0                                            ||
||                                                                            ||
||                    Unmapped : 0                                            ||
||                                                                            ||
||                   Junctions : 0                                            ||
||                      Indels : 1                                            ||
||                                                                            ||
||                Running time : 0.6 minutes                                  ||
||                                                                            ||
\\============================================================================//

May 04 8:40:39 AM Calculating Mappability Exclusion regions from: F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
May 04 8:40:44 AM Reference generated without non-polyA reference
May 04 8:40:44 AM Reference generated without Mappability reference
May 04 8:40:44 AM Reference generated without Blacklist exclusion
May 04 8:40:44 AM Converting FASTA to local TwoBitFile...done
May 04 8:40:45 AM Connecting to genome TwoBitFile...done
May 04 8:40:45 AM Making local copy of GTF file...done
May 04 8:40:46 AM Reading source GTF file...done
May 04 8:40:47 AM Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
May 04 8:40:48 AM Gene ontology not prepared for this reference
May 04 8:40:50 AM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
May 04 8:40:54 AM 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
May 04 8:41:02 AM Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
done
May 04 8:41:05 AM 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
May 04 8:41:06 AM Splice Annotations Filtered
May 04 8:41:08 AM Translating Alternate Splice Peptides...done
May 04 8:41:08 AM Splice Annotations finished

Reference build finished
May 04 8:41:09 AM Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\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
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H003.bam processed (476 milliseconds)
May 04 8:41:10 AM Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H003.bam
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Compiling data from threads
Performing final sort of fragment maps
Writing COV file
**************************************************|
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H003.bam processed (403 milliseconds)
May 04 8:41:10 AM Reference generated without non-polyA reference
May 04 8:41:10 AM Reference generated without Mappability reference
May 04 8:41:10 AM Reference generated without Blacklist exclusion
May 04 8:41:10 AM Converting FASTA to local TwoBitFile...done
May 04 8:41:12 AM Connecting to genome TwoBitFile...done
May 04 8:41:12 AM Making local copy of GTF file...done
May 04 8:41:12 AM Reading source GTF file...done
May 04 8:41:13 AM Processing gtf file...
...genes
...transcripts
...CDS
May 04 8:41:13 AM 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
May 04 8:41:14 AM Gene ontology not prepared for this reference
May 04 8:41:16 AM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
May 04 8:41:21 AM 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
May 04 8:41:29 AM 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
May 04 8:41:30 AM Splice Annotations Filtered
Reference build finished
May 04 8:41:33 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H003.bam processed (509 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H025.bam processed (337 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H026.bam processed (662 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H033.bam processed (638 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H043.bam processed (403 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H046.bam processed (3421 milliseconds)
May 04 8:41:40 AM Validating Experiment; checking COV files...
May 04 8:41:40 AM Compiling Sample Stats
May 04 8:41:41 AM Compiling Junction List...merging...done
May 04 8:41:42 AM Compiling Junction Stats...merging...done
May 04 8:41:51 AM Compiling Intron Retention List...done
May 04 8:41:52 AM Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

May 04 8:42:04 AM Generating NxtSE assays
May 04 8:42:21 AM Building Final NxtSE Object
May 04 8:42:21 AM ...consolidating assays to H5 file
May 04 8:42:24 AM ...packaging reference
May 04 8:42:24 AM ...synthesising NxtSE
May 04 8:42:24 AM ...determining how overlapping introns should be removed
May 04 8:42:27 AM SpliceWiz (NxtSE) Collation Finished
May 04 8:42:27 AM Loading NxtSE object from file...
May 04 8:42:27 AM ...loading reference (NxtSE)
May 04 8:42:27 AM ...linking assays
May 04 8:42:27 AM ...linking COV files
May 04 8:42:27 AM ...loading rowData
May 04 8:42:28 AM ...removing overlapping introns...
May 04 8:42:28 AM NxtSE loaded
May 04 8:42:28 AM SpliceWiz reference already exists in given directory
May 04 8:42:28 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H003.bam processed (512 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H025.bam processed (413 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H026.bam processed (668 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H033.bam processed (670 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H043.bam processed (428 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H046.bam processed (536 milliseconds)
May 04 8:42:32 AM Validating Experiment; checking COV files...
May 04 8:42:32 AM Compiling Sample Stats
May 04 8:42:32 AM Compiling Junction List...merging...done
May 04 8:42:33 AM Compiling Junction Stats...merging...done
May 04 8:42:42 AM Compiling Intron Retention List...done
May 04 8:42:43 AM Compiling Tandem Junction List...merging...done
May 04 8:42:45 AM Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
May 04 8:42:48 AM Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
May 04 8:43:02 AM Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

May 04 8:43:11 AM Generating NxtSE assays
May 04 8:43:28 AM Building Final NxtSE Object
May 04 8:43:28 AM ...consolidating assays to H5 file
May 04 8:43:31 AM ...packaging reference
May 04 8:43:31 AM ...synthesising NxtSE
May 04 8:43:31 AM ...determining how overlapping introns should be removed
May 04 8:43:35 AM SpliceWiz (NxtSE) Collation Finished
May 04 8:43:35 AM Loading NxtSE object from file...
May 04 8:43:35 AM ...loading reference (NxtSE)
May 04 8:43:35 AM ...linking assays
May 04 8:43:35 AM ...linking COV files
May 04 8:43:35 AM ...loading rowData
May 04 8:43:35 AM ...removing overlapping introns...
May 04 8:43:35 AM NxtSE loaded
May 04 8:43:36 AM SpliceWiz reference already exists in given directory
May 04 8:43:36 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H003.bam processed (500 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H025.bam processed (376 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H026.bam processed (664 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H033.bam processed (651 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H043.bam processed (429 milliseconds)
F:\biocbuild\bbs-3.19-bioc\tmpdir\RtmpsLx0qJ\02H046.bam processed (583 milliseconds)
May 04 8:43:39 AM Validating Experiment; checking COV files...
May 04 8:43:39 AM Compiling Sample Stats
May 04 8:43:39 AM Compiling Junction List...merging...done
May 04 8:43:41 AM Compiling Junction Stats...merging...done
May 04 8:43:49 AM Compiling Intron Retention List...done
May 04 8:43:50 AM Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

May 04 8:44:02 AM Generating NxtSE assays
May 04 8:44:20 AM Building Final NxtSE Object
May 04 8:44:20 AM ...consolidating assays to H5 file
May 04 8:44:22 AM ...packaging reference
May 04 8:44:22 AM ...synthesising NxtSE
May 04 8:44:23 AM ...determining how overlapping introns should be removed
May 04 8:44:26 AM SpliceWiz (NxtSE) Collation Finished
May 04 8:44:26 AM Loading NxtSE object from file...
May 04 8:44:26 AM ...loading reference (NxtSE)
May 04 8:44:26 AM ...linking assays
May 04 8:44:26 AM ...linking COV files
May 04 8:44:26 AM ...loading rowData
May 04 8:44:26 AM ...removing overlapping introns...
May 04 8:44:27 AM 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
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 45 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
   user  system elapsed 
 278.06   14.81  302.76 

Example timings

SpliceWiz.Rcheck/SpliceWiz-Ex.timings

nameusersystemelapsed
ASE-GLM-edgeR2.900.183.10
ASE-methods31.98 0.2232.24
ASEFilter-class0.080.020.10
Build-Reference-methods59.58 2.2869.73
Coverage0.900.011.00
Gene-ontology-methods1.830.131.92
Graphics-User-Interface000
Mappability-methods2.720.033.50
NxtSE-class56.64 2.0559.44
Run_SpliceWiz_Filters8.640.018.65
STAR-methods000
View-Reference-methods0.170.050.22
collateData0.530.050.58
coord2GR0.030.000.03
covDataObject-class1.700.041.75
covPlotObject-class25.10 0.7225.83
covPlotly-class1.340.031.37
example-SpliceWiz-data0.020.000.02
findSamples0.030.000.03
isCOV0.000.040.03
makeSE0.750.150.91
make_plot_data0.050.000.04
plotCoverage15.21 0.3115.55
processBAM2.660.341.90
setSWthreads000
theme_white0.190.000.19