Back to Multiple platform build/check report for BioC 3.17:   simplified   long
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This page was generated on 2023-10-16 11:37:34 -0400 (Mon, 16 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.2 LTS)x86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4626
palomino3Windows Server 2022 Datacenterx644.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" 4379
merida1macOS 12.6.4 Montereyx86_644.3.1 (2023-06-16) -- "Beagle Scouts" 4395
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 1993/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpliceWiz 1.2.3  (landing page)
Alex Chit Hei Wong
Snapshot Date: 2023-10-15 14:00:13 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/SpliceWiz
git_branch: RELEASE_3_17
git_last_commit: 92135a4
git_last_commit_date: 2023-07-30 17:48:22 -0400 (Sun, 30 Jul 2023)
nebbiolo1Linux (Ubuntu 22.04.2 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
merida1macOS 12.6.4 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson2macOS 12.6.1 Monterey / arm64see weekly results here

CHECK results for SpliceWiz on merida1


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: 1.2.3
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_1.2.3.tar.gz
StartedAt: 2023-10-16 07:30:53 -0400 (Mon, 16 Oct 2023)
EndedAt: 2023-10-16 08:09:14 -0400 (Mon, 16 Oct 2023)
EllapsedTime: 2300.4 seconds
RetCode: 0
Status:   OK  
CheckDir: SpliceWiz.Rcheck
Warnings: 0

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_1.2.3.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.2.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpliceWiz’ can be installed ... OK
* used C++ compiler: ‘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 ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking 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 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 126.503  3.198 167.689
NxtSE-class              70.798  1.602  97.818
ASE-methods              46.947  0.667  59.477
covPlotObject-class      38.913  0.601  50.231
plotCoverage             28.927  0.230  39.435
Run_SpliceWiz_Filters     8.737  0.038  11.153
processBAM                6.076  1.315   5.944
ASE-GLM-edgeR             5.105  0.142   6.452
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-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/4.3-x86_64/Resources/library’
* installing *source* package ‘SpliceWiz’ ...
** 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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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 -single_module -multiply_defined suppress -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 -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-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)

Tests output

SpliceWiz.Rcheck/tests/testthat.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 1 threads
Use setSWthreads() to set the number of SpliceWiz threads
> 
> test_check("SpliceWiz")
Loading required package: Rsubread
Oct 16 07:52:17 Converting FASTA to local TwoBitFile...done
Oct 16 07:52:19 Connecting to genome TwoBitFile...done
Oct 16 07:52:19 Making local copy of GTF file...done
Oct 16 07:52:19 Extracting temp genome FASTA from TwoBit file
Oct 16 07:52:21 Generating synthetic reads, saving to /private/tmp/RtmpRakHCG/refWithMapExcl/Mappability/Reads.fa
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Oct 16 07:52:21 Cleaning temp genome / gene annotation files

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.14.2

//================================= setting ==================================\\
||                                                                            ||
||                Index name : reference_index                                ||
||               Index space : base space                                     ||
||               Index split : no-split                                       ||
||          Repeat threshold : 100 repeats                                    ||
||              Gapped index : no                                             ||
||                                                                            ||
||       Free / total memory : 30.3GB / 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=18.5k bps/s                                  ||
||   16%,   0 mins elapsed, rate=36.5k bps/s                                  ||
||   24%,   0 mins elapsed, rate=54.2k bps/s                                  ||
||   33%,   0 mins elapsed, rate=71.7k bps/s                                  ||
||   41%,   0 mins elapsed, rate=88.1k bps/s                                  ||
||   49%,   0 mins elapsed, rate=104.9k bps/s                                 ||
||   58%,   0 mins elapsed, rate=121.0k bps/s                                 ||
||   66%,   0 mins elapsed, rate=137.3k bps/s                                 ||
||   74%,   0 mins elapsed, rate=153.4k bps/s                                 ||
||   83%,   0 mins elapsed, rate=168.0k bps/s                                 ||
||   91%,   0 mins elapsed, rate=183.6k bps/s                                 ||
|| 3.0 GB of memory is needed for index building.                             ||
|| Build the index...                                                         ||
||    8%,   0 mins elapsed, rate=2.0k bps/s                                   ||
||   16%,   0 mins elapsed, rate=4.0k bps/s                                   ||
||   24%,   0 mins elapsed, rate=6.0k bps/s                                   ||
||   33%,   0 mins elapsed, rate=8.0k bps/s                                   ||
||   41%,   0 mins elapsed, rate=10.0k bps/s                                  ||
||   49%,   0 mins elapsed, rate=12.0k bps/s                                  ||
||   58%,   0 mins elapsed, rate=14.0k bps/s                                  ||
||   66%,   0 mins elapsed, rate=16.0k bps/s                                  ||
||   74%,   0 mins elapsed, rate=18.0k bps/s                                  ||
||   83%,   0 mins elapsed, rate=19.9k bps/s                                  ||
||   91%,   0 mins elapsed, rate=21.9k 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: 0.8 minutes.                      ||
||              Index ./reference_index was successfully built.               ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.14.2

//================================= setting ==================================\\
||                                                                            ||
|| Function      : Read alignment + Junction detection (RNA-Seq)              ||
|| Input file    : Reads.fa                                                   ||
|| Output file   : AlignedReads.bam (BAM)                                     ||
|| Index name    : reference_index                                            ||
||                                                                            ||
||                    ------------------------------------                    ||
||                                                                            ||
||                               Threads : 1                                  ||
||                          Phred offset : 33                                 ||
||                             Min votes : 1 / 14                             ||
||                        Max mismatches : 3                                  ||
||                      Max indel length : 5                                  ||
||            Report multi-mapping reads : yes                                ||
|| Max alignments per multi-mapping read : 1                                  ||
||                           Annotations : transcripts.gtf (GTF)              ||
||                                                                            ||
\\============================================================================//

//================ Running (16-Oct-2023 07:53:07, pid=88784) =================\\
||                                                                            ||
|| 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,  11 mins elapsed, rate=15.7k reads per second             ||
||   83% completed,  11 mins elapsed, rate=0.0k reads per second              ||
||   99% completed,  11 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 : 11.9 minutes                                 ||
||                                                                            ||
\\============================================================================//

Oct 16 08:05:00 Calculating Mappability Exclusion regions from: /tmp/RtmpRakHCG/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmpRakHCG/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 16 08:05:08 Reference generated without non-polyA reference
Oct 16 08:05:08 Reference generated without Mappability reference
Oct 16 08:05:08 Reference generated without Blacklist exclusion
Oct 16 08:05:08 Converting FASTA to local TwoBitFile...done
Oct 16 08:05:09 Connecting to genome TwoBitFile...done
Oct 16 08:05:09 Making local copy of GTF file...done
Oct 16 08:05:10 Reading source GTF file...done
Oct 16 08:05:10 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 16 08:05:14 Gene ontology not prepared for this reference
Oct 16 08:05:17 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Oct 16 08:05:24 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 16 08:05:38 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
  |                                                                      |   0%
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  |======================================================================| 100%
done
Oct 16 08:05:42 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 16 08:05:44 Splice Annotations Filtered
Oct 16 08:05:45 Translating Alternate Splice Peptides...done
Oct 16 08:05:46 Splice Annotations finished

Reference build finished
Oct 16 08:05:48 Running SpliceWiz processBAM
Oct 16 08:05:49 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/RtmpRakHCG/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/RtmpRakHCG/02H003.bam processed (941 milliseconds)
Oct 16 08:05:50 SpliceWiz processBAM processed RtmpRakHCG/02H003.bam
Oct 16 08:05:50 Running SpliceWiz processBAM
Oct 16 08:05:52 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (4 milliseconds)
Processing BAM file /private/tmp/RtmpRakHCG/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/RtmpRakHCG/02H003.bam processed (944 milliseconds)
Oct 16 08:05:53 SpliceWiz processBAM processed RtmpRakHCG/02H003.bam
Oct 16 08:05:53 SpliceWiz reference already exists in given directory
Oct 16 08:05:53 Running SpliceWiz processBAM
Oct 16 08:05:54 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H003.bam processed (912 milliseconds)
Oct 16 08:05:55 SpliceWiz processBAM processed RtmpRakHCG/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (3 milliseconds)
/private/tmp/RtmpRakHCG/02H025.bam processed (774 milliseconds)
Oct 16 08:05:56 SpliceWiz processBAM processed RtmpRakHCG/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H026.bam processed (1220 milliseconds)
Oct 16 08:05:57 SpliceWiz processBAM processed RtmpRakHCG/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H033.bam processed (1135 milliseconds)
Oct 16 08:05:59 SpliceWiz processBAM processed RtmpRakHCG/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H043.bam processed (718 milliseconds)
Oct 16 08:05:59 SpliceWiz processBAM processed RtmpRakHCG/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H046.bam processed (1016 milliseconds)
Oct 16 08:06:00 SpliceWiz processBAM processed RtmpRakHCG/02H046.bam
Oct 16 08:06:02 Using MulticoreParam 1 threads
Oct 16 08:06:02 Validating Experiment; checking COV files...
Oct 16 08:06:02 Compiling Sample Stats
Oct 16 08:06:02 Compiling Junction List...merging...done
Oct 16 08:06:04 Compiling Junction Stats...merging...done
Oct 16 08:06:14 Compiling Intron Retention List...done
Oct 16 08:06:16 Compiling Tandem Junction List...merging...done
Oct 16 08:06:17 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Oct 16 08:06:22 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 16 08:06:41 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Oct 16 08:06:54 Generating NxtSE assays
Oct 16 08:06:55 Using MulticoreParam 1 threads

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Oct 16 08:07:18 Building Final NxtSE Object
Oct 16 08:07:18 ...consolidating assays to H5 file
Oct 16 08:07:21 ...packaging reference
Oct 16 08:07:21 ...synthesising NxtSE
Oct 16 08:07:22 ...determining how overlapping introns should be removed
Oct 16 08:07:31 SpliceWiz (NxtSE) Collation Finished
Oct 16 08:07:31 Loading NxtSE object from file...
Oct 16 08:07:31 ...loading reference (NxtSE)
Oct 16 08:07:31 ...linking assays
Oct 16 08:07:31 ...linking COV files
Oct 16 08:07:31 ...loading rowData
Oct 16 08:07:31 ...removing overlapping introns...
Oct 16 08:07:31 NxtSE loaded
Oct 16 08:07:32 SpliceWiz reference already exists in given directory
Oct 16 08:07:32 Running SpliceWiz processBAM
Oct 16 08:07:34 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H003.bam processed (977 milliseconds)
Oct 16 08:07:35 SpliceWiz processBAM processed RtmpRakHCG/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H025.bam processed (765 milliseconds)
Oct 16 08:07:36 SpliceWiz processBAM processed RtmpRakHCG/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H026.bam processed (1121 milliseconds)
Oct 16 08:07:37 SpliceWiz processBAM processed RtmpRakHCG/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H033.bam processed (1145 milliseconds)
Oct 16 08:07:38 SpliceWiz processBAM processed RtmpRakHCG/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmpRakHCG/02H043.bam processed (708 milliseconds)
Oct 16 08:07:39 SpliceWiz processBAM processed RtmpRakHCG/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (5 milliseconds)
/private/tmp/RtmpRakHCG/02H046.bam processed (1116 milliseconds)
Oct 16 08:07:40 SpliceWiz processBAM processed RtmpRakHCG/02H046.bam
Oct 16 08:07:41 Using MulticoreParam 1 threads
Oct 16 08:07:41 Validating Experiment; checking COV files...
Oct 16 08:07:41 Compiling Sample Stats
Oct 16 08:07:42 Compiling Junction List...merging...done
Oct 16 08:07:43 Compiling Junction Stats...merging...done
Oct 16 08:07:54 Compiling Intron Retention List...done
Oct 16 08:07:55 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 16 08:08:12 Generating NxtSE assays
Oct 16 08:08:14 Using MulticoreParam 1 threads

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Oct 16 08:08:37 Building Final NxtSE Object
Oct 16 08:08:37 ...consolidating assays to H5 file
Oct 16 08:08:40 ...packaging reference
Oct 16 08:08:40 ...synthesising NxtSE
Oct 16 08:08:41 ...determining how overlapping introns should be removed
Oct 16 08:08:50 SpliceWiz (NxtSE) Collation Finished
Oct 16 08:08:50 Loading NxtSE object from file...
Oct 16 08:08:50 ...loading reference (NxtSE)
Oct 16 08:08:50 ...linking assays
Oct 16 08:08:50 ...linking COV files
Oct 16 08:08:50 ...loading rowData
Oct 16 08:08:50 ...removing overlapping introns...
Oct 16 08:08:50 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
    user   system  elapsed 
 457.721  331.174 1032.612 

Example timings

SpliceWiz.Rcheck/SpliceWiz-Ex.timings

nameusersystemelapsed
ASE-GLM-edgeR5.1050.1426.452
ASE-methods46.947 0.66759.477
ASEFilter-class0.1110.0080.147
Build-Reference-methods126.503 3.198167.689
Coverage1.9830.0552.707
Gene-ontology-methods2.5780.0863.522
Graphics-User-Interface0.0010.0010.001
Mappability-methods2.6400.0673.555
NxtSE-class70.798 1.60297.818
Run_SpliceWiz_Filters 8.737 0.03811.153
STAR-methods0.0070.0160.040
View-Reference-methods0.2910.0310.395
collateData3.1240.0904.276
coord2GR0.0480.0030.067
covDataObject-class3.2750.0514.250
covPlotObject-class38.913 0.60150.231
covPlotly-class2.3150.0273.008
example-SpliceWiz-data0.0260.0040.038
findSamples0.0110.0070.023
isCOV0.0250.0060.041
makeSE2.5860.1403.710
make_plot_data0.1070.0050.159
plotCoverage28.927 0.23039.435
processBAM6.0761.3155.944
setSWthreads0.0040.0180.028
theme_white0.3100.0960.469