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This page was generated on 2024-04-17 11:38:17 -0400 (Wed, 17 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4676
palomino4Windows Server 2022 Datacenterx644.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" 4414
merida1macOS 12.7.1 Montereyx86_644.3.3 (2024-02-29) -- "Angel Food Cake" 4437
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 2030/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpliceWiz 1.4.1  (landing page)
Alex Chit Hei Wong
Snapshot Date: 2024-04-15 14:05:01 -0400 (Mon, 15 Apr 2024)
git_url: https://git.bioconductor.org/packages/SpliceWiz
git_branch: RELEASE_3_18
git_last_commit: e98216c
git_last_commit_date: 2024-01-04 23:20:45 -0400 (Thu, 04 Jan 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino4Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.1 Ventura / 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: 1.4.1
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.4.1.tar.gz
StartedAt: 2024-04-16 09:22:13 -0400 (Tue, 16 Apr 2024)
EndedAt: 2024-04-16 09:56:13 -0400 (Tue, 16 Apr 2024)
EllapsedTime: 2040.1 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_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.4.1’
* 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 126.700  3.017 144.084
NxtSE-class              65.998  1.551  71.260
ASE-methods              47.869  0.516  50.874
covPlotObject-class      44.025  0.785  54.701
plotCoverage             30.269  0.402  33.177
Run_SpliceWiz_Filters     9.114  0.050   9.690
processBAM                6.240  1.321   5.232
ASE-GLM-edgeR             5.135  0.175   5.365
* 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-3.18-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 -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 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 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
Apr 16 09:40:46 Converting FASTA to local TwoBitFile...done
Apr 16 09:40:47 Connecting to genome TwoBitFile...done
Apr 16 09:40:47 Making local copy of GTF file...done
Apr 16 09:40:48 Extracting temp genome FASTA from TwoBit file
Apr 16 09:40:49 Generating synthetic reads, saving to /private/tmp/RtmphXoSme/refWithMapExcl/Mappability/Reads.fa
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Apr 16 09:40:49 Cleaning temp genome / gene annotation files

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.16.1

//================================= setting ==================================\\
||                                                                            ||
||                Index name : reference_index                                ||
||               Index space : base space                                     ||
||               Index split : no-split                                       ||
||          Repeat threshold : 100 repeats                                    ||
||              Gapped index : no                                             ||
||                                                                            ||
||       Free / total memory : 35.8GB / 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=23.6k bps/s                                  ||
||   16%,   0 mins elapsed, rate=46.7k bps/s                                  ||
||   24%,   0 mins elapsed, rate=69.0k bps/s                                  ||
||   33%,   0 mins elapsed, rate=91.2k bps/s                                  ||
||   41%,   0 mins elapsed, rate=112.5k bps/s                                 ||
||   49%,   0 mins elapsed, rate=133.7k bps/s                                 ||
||   58%,   0 mins elapsed, rate=154.6k bps/s                                 ||
||   66%,   0 mins elapsed, rate=174.4k bps/s                                 ||
||   74%,   0 mins elapsed, rate=194.0k bps/s                                 ||
||   83%,   0 mins elapsed, rate=213.4k bps/s                                 ||
||   91%,   0 mins elapsed, rate=230.6k bps/s                                 ||
|| 3.0 GB of memory is needed for index building.                             ||
|| Build the index...                                                         ||
||    8%,   0 mins elapsed, rate=2.5k bps/s                                   ||
||   16%,   0 mins elapsed, rate=4.9k bps/s                                   ||
||   24%,   0 mins elapsed, rate=7.4k bps/s                                   ||
||   33%,   0 mins elapsed, rate=9.9k bps/s                                   ||
||   41%,   0 mins elapsed, rate=12.3k bps/s                                  ||
||   49%,   0 mins elapsed, rate=14.8k bps/s                                  ||
||   58%,   0 mins elapsed, rate=17.2k bps/s                                  ||
||   66%,   0 mins elapsed, rate=19.6k bps/s                                  ||
||   74%,   0 mins elapsed, rate=22.0k bps/s                                  ||
||   83%,   0 mins elapsed, rate=24.4k bps/s                                  ||
||   91%,   0 mins elapsed, rate=26.8k 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: 0.7 minutes.                      ||
||              Index ./reference_index was successfully built.               ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.16.1

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

//================ Running (16-Apr-2024 09:41:30, pid=22073) =================\\
||                                                                            ||
|| 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,  10 mins elapsed, rate=17.7k reads per second             ||
||   83% completed,  10 mins elapsed, rate=0.0k reads per second              ||
||   99% completed,  10 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 : 10.0 minutes                                 ||
||                                                                            ||
\\============================================================================//

Apr 16 09:51:32 Calculating Mappability Exclusion regions from: /tmp/RtmphXoSme/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmphXoSme/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
Apr 16 09:51:39 Reference generated without non-polyA reference
Apr 16 09:51:39 Reference generated without Mappability reference
Apr 16 09:51:39 Reference generated without Blacklist exclusion
Apr 16 09:51:39 Converting FASTA to local TwoBitFile...done
Apr 16 09:51:40 Connecting to genome TwoBitFile...done
Apr 16 09:51:40 Making local copy of GTF file...done
Apr 16 09:51:41 Reading source GTF file...done
Apr 16 09:51:41 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 16 09:51:44 Gene ontology not prepared for this reference
Apr 16 09:51:46 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 16 09:51:52 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
Apr 16 09:52:03 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |======================================================================| 100%
done
Apr 16 09:52:06 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Apr 16 09:52:08 Splice Annotations Filtered
Apr 16 09:52:09 Translating Alternate Splice Peptides...done
Apr 16 09:52:09 Splice Annotations finished

Reference build finished
Apr 16 09:52:11 Running SpliceWiz processBAM
Apr 16 09:52:12 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/RtmphXoSme/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/RtmphXoSme/02H003.bam processed (740 milliseconds)
Apr 16 09:52:13 SpliceWiz processBAM processed RtmphXoSme/02H003.bam
Apr 16 09:52:13 Running SpliceWiz processBAM
Apr 16 09:52:14 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/RtmphXoSme/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/RtmphXoSme/02H003.bam processed (720 milliseconds)
Apr 16 09:52:15 SpliceWiz processBAM processed RtmphXoSme/02H003.bam
Apr 16 09:52:15 Reference generated without non-polyA reference
Apr 16 09:52:15 Reference generated without Mappability reference
Apr 16 09:52:15 Reference generated without Blacklist exclusion
Apr 16 09:52:15 Converting FASTA to local TwoBitFile...done
Apr 16 09:52:16 Connecting to genome TwoBitFile...done
Apr 16 09:52:16 Making local copy of GTF file...done
Apr 16 09:52:17 Reading source GTF file...done
Apr 16 09:52:17 Processing gtf file...
...genes
...transcripts
...CDS
Apr 16 09:52:18 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
Apr 16 09:52:19 Gene ontology not prepared for this reference
Apr 16 09:52:21 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 16 09:52:27 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
Apr 16 09:52:37 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
Apr 16 09:52:38 Splice Annotations Filtered
Reference build finished
Apr 16 09:52:41 Running SpliceWiz processBAM
Apr 16 09:52:42 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H003.bam processed (711 milliseconds)
Apr 16 09:52:43 SpliceWiz processBAM processed RtmphXoSme/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H025.bam processed (578 milliseconds)
Apr 16 09:52:43 SpliceWiz processBAM processed RtmphXoSme/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H026.bam processed (883 milliseconds)
Apr 16 09:52:44 SpliceWiz processBAM processed RtmphXoSme/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H033.bam processed (884 milliseconds)
Apr 16 09:52:45 SpliceWiz processBAM processed RtmphXoSme/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H043.bam processed (576 milliseconds)
Apr 16 09:52:46 SpliceWiz processBAM processed RtmphXoSme/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H046.bam processed (811 milliseconds)
Apr 16 09:52:47 SpliceWiz processBAM processed RtmphXoSme/02H046.bam
Apr 16 09:52:48 Using MulticoreParam 1 threads
Apr 16 09:52:48 Validating Experiment; checking COV files...
Apr 16 09:52:48 Compiling Sample Stats
Apr 16 09:52:48 Compiling Junction List...merging...done
Apr 16 09:52:49 Compiling Junction Stats...merging...done
Apr 16 09:52:57 Compiling Intron Retention List...done
Apr 16 09:52:59 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Apr 16 09:53:12 Generating NxtSE assays
Apr 16 09:53:13 Using MulticoreParam 1 threads

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Apr 16 09:53:32 Building Final NxtSE Object
Apr 16 09:53:32 ...consolidating assays to H5 file
Apr 16 09:53:34 ...packaging reference
Apr 16 09:53:34 ...synthesising NxtSE
Apr 16 09:53:34 ...determining how overlapping introns should be removed
Apr 16 09:53:38 SpliceWiz (NxtSE) Collation Finished
Apr 16 09:53:38 Loading NxtSE object from file...
Apr 16 09:53:38 ...loading reference (NxtSE)
Apr 16 09:53:38 ...linking assays
Apr 16 09:53:38 ...linking COV files
Apr 16 09:53:38 ...loading rowData
Apr 16 09:53:38 ...removing overlapping introns...
Apr 16 09:53:38 NxtSE loaded
Apr 16 09:53:39 SpliceWiz reference already exists in given directory
Apr 16 09:53:39 Running SpliceWiz processBAM
Apr 16 09:53:41 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H003.bam processed (730 milliseconds)
Apr 16 09:53:41 SpliceWiz processBAM processed RtmphXoSme/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H025.bam processed (570 milliseconds)
Apr 16 09:53:42 SpliceWiz processBAM processed RtmphXoSme/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H026.bam processed (940 milliseconds)
Apr 16 09:53:43 SpliceWiz processBAM processed RtmphXoSme/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (2 milliseconds)
/private/tmp/RtmphXoSme/02H033.bam processed (878 milliseconds)
Apr 16 09:53:44 SpliceWiz processBAM processed RtmphXoSme/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (2 milliseconds)
/private/tmp/RtmphXoSme/02H043.bam processed (559 milliseconds)
Apr 16 09:53:44 SpliceWiz processBAM processed RtmphXoSme/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H046.bam processed (818 milliseconds)
Apr 16 09:53:45 SpliceWiz processBAM processed RtmphXoSme/02H046.bam
Apr 16 09:53:46 Using MulticoreParam 1 threads
Apr 16 09:53:46 Validating Experiment; checking COV files...
Apr 16 09:53:46 Compiling Sample Stats
Apr 16 09:53:47 Compiling Junction List...merging...done
Apr 16 09:53:48 Compiling Junction Stats...merging...done
Apr 16 09:53:56 Compiling Intron Retention List...done
Apr 16 09:53:58 Compiling Tandem Junction List...merging...done
Apr 16 09:53:59 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Apr 16 09:54:03 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Apr 16 09:54:18 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Apr 16 09:54:28 Generating NxtSE assays
Apr 16 09:54:29 Using MulticoreParam 1 threads

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Apr 16 09:54:49 Building Final NxtSE Object
Apr 16 09:54:49 ...consolidating assays to H5 file
Apr 16 09:54:51 ...packaging reference
Apr 16 09:54:51 ...synthesising NxtSE
Apr 16 09:54:51 ...determining how overlapping introns should be removed
Apr 16 09:54:54 SpliceWiz (NxtSE) Collation Finished
Apr 16 09:54:54 Loading NxtSE object from file...
Apr 16 09:54:54 ...loading reference (NxtSE)
Apr 16 09:54:54 ...linking assays
Apr 16 09:54:55 ...linking COV files
Apr 16 09:54:55 ...loading rowData
Apr 16 09:54:55 ...removing overlapping introns...
Apr 16 09:54:55 NxtSE loaded
Apr 16 09:54:56 SpliceWiz reference already exists in given directory
Apr 16 09:54:56 Running SpliceWiz processBAM
Apr 16 09:54:57 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H003.bam processed (730 milliseconds)
Apr 16 09:54:58 SpliceWiz processBAM processed RtmphXoSme/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H025.bam processed (581 milliseconds)
Apr 16 09:54:58 SpliceWiz processBAM processed RtmphXoSme/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H026.bam processed (882 milliseconds)
Apr 16 09:54:59 SpliceWiz processBAM processed RtmphXoSme/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H033.bam processed (884 milliseconds)
Apr 16 09:55:00 SpliceWiz processBAM processed RtmphXoSme/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H043.bam processed (570 milliseconds)
Apr 16 09:55:01 SpliceWiz processBAM processed RtmphXoSme/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/RtmphXoSme/02H046.bam processed (804 milliseconds)
Apr 16 09:55:01 SpliceWiz processBAM processed RtmphXoSme/02H046.bam
Apr 16 09:55:03 Using MulticoreParam 1 threads
Apr 16 09:55:03 Validating Experiment; checking COV files...
Apr 16 09:55:03 Compiling Sample Stats
Apr 16 09:55:03 Compiling Junction List...merging...done
Apr 16 09:55:04 Compiling Junction Stats...merging...done
Apr 16 09:55:13 Compiling Intron Retention List...done
Apr 16 09:55:14 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Apr 16 09:55:27 Generating NxtSE assays
Apr 16 09:55:29 Using MulticoreParam 1 threads

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Apr 16 09:55:48 Building Final NxtSE Object
Apr 16 09:55:48 ...consolidating assays to H5 file
Apr 16 09:55:50 ...packaging reference
Apr 16 09:55:50 ...synthesising NxtSE
Apr 16 09:55:50 ...determining how overlapping introns should be removed
Apr 16 09:55:54 SpliceWiz (NxtSE) Collation Finished
Apr 16 09:55:54 Loading NxtSE object from file...
Apr 16 09:55:54 ...loading reference (NxtSE)
Apr 16 09:55:54 ...linking assays
Apr 16 09:55:54 ...linking COV files
Apr 16 09:55:54 ...loading rowData
Apr 16 09:55:54 ...removing overlapping introns...
Apr 16 09:55:54 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
   user  system elapsed 
531.876 336.067 941.552 

Example timings

SpliceWiz.Rcheck/SpliceWiz-Ex.timings

nameusersystemelapsed
ASE-GLM-edgeR5.1350.1755.365
ASE-methods47.869 0.51650.874
ASEFilter-class0.1040.0070.123
Build-Reference-methods126.700 3.017144.084
Coverage1.9270.0512.147
Gene-ontology-methods3.8380.1184.313
Graphics-User-Interface0.0000.0010.002
Mappability-methods2.6100.0663.070
NxtSE-class65.998 1.55171.260
Run_SpliceWiz_Filters9.1140.0509.690
STAR-methods0.0070.0160.044
View-Reference-methods0.3010.0360.380
collateData3.1900.0863.495
coord2GR0.0470.0030.052
covDataObject-class3.4720.0493.742
covPlotObject-class44.025 0.78554.701
covPlotly-class2.2050.0462.328
example-SpliceWiz-data0.0270.0070.043
findSamples0.0110.0080.021
isCOV0.0250.0050.034
makeSE2.4940.1512.754
make_plot_data0.1040.0060.114
plotCoverage30.269 0.40233.177
processBAM6.2401.3215.232
setSWthreads0.0040.0170.026
theme_white0.2950.1010.400