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This page was generated on 2025-09-13 12:03 -0400 (Sat, 13 Sep 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4719
lconwaymacOS 12.7.1 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4538
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4522
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4543
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 2073/2327HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SpliceWiz 1.11.0  (landing page)
Alex Chit Hei Wong
Snapshot Date: 2025-09-12 13:45 -0400 (Fri, 12 Sep 2025)
git_url: https://git.bioconductor.org/packages/SpliceWiz
git_branch: devel
git_last_commit: ff5b222
git_last_commit_date: 2025-04-15 12:53:12 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 Ventura / arm64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    ERROR  


CHECK results for SpliceWiz on nebbiolo2

To the developers/maintainers of the SpliceWiz package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceWiz.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: SpliceWiz
Version: 1.11.0
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SpliceWiz_1.11.0.tar.gz
StartedAt: 2025-09-13 04:24:35 -0400 (Sat, 13 Sep 2025)
EndedAt: 2025-09-13 04:44:08 -0400 (Sat, 13 Sep 2025)
EllapsedTime: 1173.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: SpliceWiz.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings SpliceWiz_1.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 44 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpliceWiz’ can be installed ... WARNING
Found the following significant warnings:
  Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
See ‘/home/biocbuild/bbs-3.22-bioc/meat/SpliceWiz.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... INFO
  installed size is 12.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   8.8Mb
* 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 loading without being on the library search path ... OK
* checking whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Non-topic package-anchored link(s) in Rd file 'ASE-methods.Rd':
  ‘[limma:toptable]{limma::topTable}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  NxtSE-class.Rd: SummarizedExperiment-class
  SpliceWiz-package.Rd: SummarizedExperiment-class, rowData, colData
  makeSE.Rd: colData
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
Build-Reference-methods 56.520  4.067  61.331
NxtSE-class             56.991  3.025  60.042
ASE-methods             31.575  3.269  34.841
covPlotObject-class     27.412  1.240  24.896
plotCoverage            16.727  1.122  17.684
Run_SpliceWiz_Filters    8.250  0.986   9.235
Gene-ontology-methods    8.138  0.255   2.538
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.


Installation output

SpliceWiz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL SpliceWiz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘SpliceWiz’ ...
** this is package ‘SpliceWiz’ version ‘1.11.0’
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c BAM2blocks.cpp -o BAM2blocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c FastaReader.cpp -o FastaReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c FragmentBlocks.cpp -o FragmentBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c GZTools.cpp -o GZTools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c covTools.cpp -o covTools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c main.cpp -o main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c swEngine.cpp -o swEngine.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.22-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.22-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -Werror=format-security  -c synthReadGenerator.cpp -o synthReadGenerator.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.22-bioc/R/lib -L/usr/local/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 -fopenmp -DSPLICEWIZ -L/home/biocbuild/bbs-3.22-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.22-bioc/R/site-library/00LOCK-SpliceWiz/00new/SpliceWiz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: The `size` argument of `element_line()` is deprecated as of ggplot2 3.4.0.
ℹ Please use the `linewidth` argument instead.
ℹ The deprecated feature was likely used in the SpliceWiz package.
  Please report the issue at <https://support.bioconductor.org/>.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpliceWiz)

Tests output

SpliceWiz.Rcheck/tests/testthat.Rout


R version 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

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 36 threads
Use setSWthreads() to set the number of SpliceWiz threads
> 
> test_check("SpliceWiz")
Loading required package: Rsubread
Sep 13 04:34:37 Converting FASTA to local TwoBitFile...done
Sep 13 04:34:39 Connecting to genome TwoBitFile...done
Sep 13 04:34:39 Making local copy of GTF file...done
Sep 13 04:34:39 Extracting temp genome FASTA from TwoBit file
Sep 13 04:34:40 Generating synthetic reads, saving to /tmp/Rtmpmlia1p/refWithMapExcl/Mappability/Reads.fa
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Sep 13 04:34:40 Cleaning temp genome / gene annotation files

        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.23.4

//================================= setting ==================================\\
||                                                                            ||
||                Index name : reference_index                                ||
||               Index space : base space                                     ||
||               Index split : no-split                                       ||
||          Repeat threshold : 100 repeats                                    ||
||              Gapped index : no                                             ||
||                                                                            ||
||       Free / total memory : 74.6GB / 125.4GB                               ||
||                                                                            ||
||               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=42.8k bps/s                                  ||
||   16%,   0 mins elapsed, rate=84.6k bps/s                                  ||
||   24%,   0 mins elapsed, rate=125.8k bps/s                                 ||
||   33%,   0 mins elapsed, rate=166.2k bps/s                                 ||
||   41%,   0 mins elapsed, rate=206.0k bps/s                                 ||
||   49%,   0 mins elapsed, rate=245.3k bps/s                                 ||
||   58%,   0 mins elapsed, rate=284.0k bps/s                                 ||
||   66%,   0 mins elapsed, rate=322.0k bps/s                                 ||
||   74%,   0 mins elapsed, rate=359.7k bps/s                                 ||
||   83%,   0 mins elapsed, rate=382.2k bps/s                                 ||
||   91%,   0 mins elapsed, rate=417.0k bps/s                                 ||
|| 3.0 GB of memory is needed for index building.                             ||
|| Build the index...                                                         ||
||    8%,   0 mins elapsed, rate=4.3k bps/s                                   ||
||   16%,   0 mins elapsed, rate=8.6k bps/s                                   ||
||   24%,   0 mins elapsed, rate=12.9k bps/s                                  ||
||   33%,   0 mins elapsed, rate=17.2k bps/s                                  ||
||   41%,   0 mins elapsed, rate=21.4k bps/s                                  ||
||   49%,   0 mins elapsed, rate=25.7k bps/s                                  ||
||   58%,   0 mins elapsed, rate=29.9k bps/s                                  ||
||   66%,   0 mins elapsed, rate=34.1k bps/s                                  ||
||   74%,   0 mins elapsed, rate=38.3k bps/s                                  ||
||   83%,   0 mins elapsed, rate=42.5k bps/s                                  ||
||   91%,   0 mins elapsed, rate=46.6k 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: 0.2 minutes.                      ||
||              Index ./reference_index was successfully built.               ||
||                                                                            ||
\\============================================================================//


        ==========     _____ _    _ ____  _____  ______          _____  
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \ 
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
       Rsubread 2.23.4

//================================= 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 (13-Sep-2025 04:34:50, pid=1243398) ================\\
||                                                                            ||
|| 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, 0.6 mins elapsed, rate=45.9k reads per second             ||
||   83% completed, 0.6 mins elapsed, rate=0.2k reads per second              ||
||   99% completed, 0.6 mins elapsed, rate=0.3k 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 : 0.6 minutes                                  ||
||                                                                            ||
\\============================================================================//

Sep 13 04:35:26 Calculating Mappability Exclusion regions from: /tmp/Rtmpmlia1p/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /tmp/Rtmpmlia1p/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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Sep 13 04:35:30 Reference generated without non-polyA reference
Sep 13 04:35:30 Reference generated without Mappability reference
Sep 13 04:35:30 Reference generated without Blacklist exclusion
Sep 13 04:35:30 Converting FASTA to local TwoBitFile...done
Sep 13 04:35:31 Connecting to genome TwoBitFile...done
Sep 13 04:35:31 Making local copy of GTF file...done
Sep 13 04:35:31 Reading source GTF file...done
Sep 13 04:35:31 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Sep 13 04:35:32 Gene ontology not prepared for this reference
Sep 13 04:35:34 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Sep 13 04:35:38 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
Sep 13 04:35:45 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
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  |======================================================================| 100%
done
Sep 13 04:35:48 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
Sep 13 04:35:49 Splice Annotations Filtered
Sep 13 04:35:50 Translating Alternate Splice Peptides...done
Sep 13 04:35:50 Splice Annotations finished

Reference build finished
Sep 13 04:35:52 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/Rtmpmlia1p/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
/tmp/Rtmpmlia1p/02H003.bam processed (377 milliseconds)
Sep 13 04:35:52 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/Rtmpmlia1p/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
/tmp/Rtmpmlia1p/02H003.bam processed (250 milliseconds)
Sep 13 04:35:52 Reference generated without non-polyA reference
Sep 13 04:35:52 Reference generated without Mappability reference
Sep 13 04:35:52 Reference generated without Blacklist exclusion
Sep 13 04:35:52 Converting FASTA to local TwoBitFile...done
Sep 13 04:35:54 Connecting to genome TwoBitFile...done
Sep 13 04:35:54 Making local copy of GTF file...done
Sep 13 04:35:54 Reading source GTF file...done
Sep 13 04:35:54 Processing gtf file...
...genes
...transcripts
...CDS
Sep 13 04:35:54 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
Sep 13 04:35:55 Gene ontology not prepared for this reference
Sep 13 04:35:57 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Sep 13 04:36:01 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Sep 13 04:36:08 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Sep 13 04:36:10 Splice Annotations Filtered
Reference build finished
Sep 13 04:36:12 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmpmlia1p/02H003.bam processed (377 milliseconds)
/tmp/Rtmpmlia1p/02H025.bam processed (298 milliseconds)
/tmp/Rtmpmlia1p/02H026.bam processed (447 milliseconds)
/tmp/Rtmpmlia1p/02H033.bam processed (449 milliseconds)
/tmp/Rtmpmlia1p/02H043.bam processed (285 milliseconds)
/tmp/Rtmpmlia1p/02H046.bam processed (421 milliseconds)
Sep 13 04:36:16 Using MulticoreParam 1 threads
Sep 13 04:36:16 Validating Experiment; checking COV files...
Sep 13 04:36:16 Compiling Sample Stats
Sep 13 04:36:16 Compiling Junction List...merging...done
Sep 13 04:36:17 Compiling Junction Stats...merging...done
Sep 13 04:36:26 Compiling Intron Retention List...done
Sep 13 04:36:27 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Sep 13 04:36:39 Generating NxtSE assays
Sep 13 04:36:40 Using MulticoreParam 1 threads

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Sep 13 04:36:56 Building Final NxtSE Object
Sep 13 04:36:56 ...consolidating assays to H5 file
Sep 13 04:36:58 ...packaging reference
Sep 13 04:36:58 ...synthesising NxtSE
Sep 13 04:36:58 ...determining how overlapping introns should be removed
Sep 13 04:37:01 SpliceWiz (NxtSE) Collation Finished
Sep 13 04:37:01 Loading NxtSE object from file...
Sep 13 04:37:01 ...loading reference (NxtSE)
Sep 13 04:37:01 ...linking assays
Sep 13 04:37:01 ...linking COV files
Sep 13 04:37:01 ...loading rowData
Sep 13 04:37:01 ...removing overlapping introns...
Sep 13 04:37:01 NxtSE loaded
Sep 13 04:37:02 SpliceWiz reference already exists in given directory
Sep 13 04:37:02 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmpmlia1p/02H003.bam processed (374 milliseconds)
/tmp/Rtmpmlia1p/02H025.bam processed (304 milliseconds)
/tmp/Rtmpmlia1p/02H026.bam processed (465 milliseconds)
/tmp/Rtmpmlia1p/02H033.bam processed (460 milliseconds)
/tmp/Rtmpmlia1p/02H043.bam processed (316 milliseconds)
/tmp/Rtmpmlia1p/02H046.bam processed (417 milliseconds)
Sep 13 04:37:05 Using MulticoreParam 1 threads
Sep 13 04:37:05 Validating Experiment; checking COV files...
Sep 13 04:37:05 Compiling Sample Stats
Sep 13 04:37:05 Compiling Junction List...merging...done
Sep 13 04:37:06 Compiling Junction Stats...merging...done
Sep 13 04:37:15 Compiling Intron Retention List...done
Sep 13 04:37:16 Compiling Tandem Junction List...merging...done
Sep 13 04:37:17 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Sep 13 04:37:21 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Sep 13 04:37:32 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Sep 13 04:37:40 Generating NxtSE assays
Sep 13 04:37:41 Using MulticoreParam 1 threads

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Sep 13 04:37:58 Building Final NxtSE Object
Sep 13 04:37:58 ...consolidating assays to H5 file
Sep 13 04:37:59 ...packaging reference
Sep 13 04:37:59 ...synthesising NxtSE
Sep 13 04:38:00 ...determining how overlapping introns should be removed
Sep 13 04:38:02 SpliceWiz (NxtSE) Collation Finished
Sep 13 04:38:02 Loading NxtSE object from file...
Sep 13 04:38:02 ...loading reference (NxtSE)
Sep 13 04:38:02 ...linking assays
Sep 13 04:38:02 ...linking COV files
Sep 13 04:38:02 ...loading rowData
Sep 13 04:38:02 ...removing overlapping introns...
Sep 13 04:38:02 NxtSE loaded
Sep 13 04:38:03 SpliceWiz reference already exists in given directory
Sep 13 04:38:03 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmpmlia1p/02H003.bam processed (365 milliseconds)
/tmp/Rtmpmlia1p/02H025.bam processed (288 milliseconds)
/tmp/Rtmpmlia1p/02H026.bam processed (452 milliseconds)
/tmp/Rtmpmlia1p/02H033.bam processed (452 milliseconds)
/tmp/Rtmpmlia1p/02H043.bam processed (283 milliseconds)
/tmp/Rtmpmlia1p/02H046.bam processed (404 milliseconds)
Sep 13 04:38:06 Using MulticoreParam 1 threads
Sep 13 04:38:06 Validating Experiment; checking COV files...
Sep 13 04:38:06 Compiling Sample Stats
Sep 13 04:38:06 Compiling Junction List...merging...done
Sep 13 04:38:07 Compiling Junction Stats...merging...done
Sep 13 04:38:15 Compiling Intron Retention List...done
Sep 13 04:38:16 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Sep 13 04:38:28 Generating NxtSE assays
Sep 13 04:38:29 Using MulticoreParam 1 threads

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Sep 13 04:38:44 Building Final NxtSE Object
Sep 13 04:38:44 ...consolidating assays to H5 file
Sep 13 04:38:46 ...packaging reference
Sep 13 04:38:46 ...synthesising NxtSE
Sep 13 04:38:46 ...determining how overlapping introns should be removed
Sep 13 04:38:49 SpliceWiz (NxtSE) Collation Finished
Sep 13 04:38:49 Loading NxtSE object from file...
Sep 13 04:38:49 ...loading reference (NxtSE)
Sep 13 04:38:49 ...linking assays
Sep 13 04:38:49 ...linking COV files
Sep 13 04:38:49 ...loading rowData
Sep 13 04:38:49 ...removing overlapping introns...
Sep 13 04:38:49 NxtSE loaded
                                    path paired strand  depth mean_frag_size
02H003 ../SpliceWiz_Output/02H003.txt.gz   TRUE     -1 106256       149.3108
02H025 ../SpliceWiz_Output/02H025.txt.gz   TRUE     -1  84872       151.5914
02H026 ../SpliceWiz_Output/02H026.txt.gz   TRUE     -1 131514       150.3238
02H033 ../SpliceWiz_Output/02H033.txt.gz   TRUE     -1 129013       153.9754
02H043 ../SpliceWiz_Output/02H043.txt.gz   TRUE     -1  80254       155.4004
02H046 ../SpliceWiz_Output/02H046.txt.gz   TRUE     -1 120174       151.2840
       directionality_strength Intergenic_Fraction rRNA_Fraction
02H003                    9850                   0             0
02H025                    9848                   0             0
02H026                    9848                   0             0
02H033                    9855                   0             0
02H043                    9841                   0             0
02H046                    9857                   0             0
       NonPolyA_Fraction Mitochondrial_Fraction Unanno_Jn_Fraction
02H003                 0                      0        0.013449472
02H025                 0                      0        0.011203515
02H026                 0                      0        0.007282382
02H033                 0                      0        0.006310241
02H043                 0                      0        0.005871040
02H046                 0                      0        0.009819533
       NMD_Jn_Fraction Fraction_Splice_Reads Fraction_Span_Reads IRBurden_clean
02H003     0.019509970             0.3506908           0.1735243     0.05796583
02H025     0.019360162             0.3712414           0.1591691     0.03963531
02H026     0.004298323             0.3980261           0.1615037     0.02576549
02H033     0.007705562             0.4003550           0.1734089     0.03090263
02H043     0.028069104             0.3671219           0.1807511     0.03762138
02H046     0.010542303             0.3725598           0.1603508     0.05099352
       IRBurden_exitrons IRBurden_clean_unstranded IRBurden_exitrons_unstranded
02H003         0.1291810                0.03844293                    0.1296020
02H025         0.1192351                0.02730399                    0.1194005
02H026         0.1231055                0.02010410                    0.1231939
02H033         0.1378958                0.02300500                    0.1380215
02H043         0.1392935                0.02286515                    0.1397365
02H046         0.1132136                0.03359077                    0.1133852
       IRBurden_antisense
02H003        0.021393335
02H025        0.013191532
02H026        0.006007119
02H033        0.008453742
02H043        0.015837096
02H046        0.019043703

MD5 is fcdc53e0f7fbd843529077ebd26dd058
Sep 13 04:38:52 Reference generated without non-polyA reference
Sep 13 04:38:52 Reference generated without Mappability reference
Sep 13 04:38:52 Reference generated without Blacklist exclusion
Sep 13 04:38:52 Converting FASTA to local TwoBitFile...done
Sep 13 04:38:53 Connecting to genome TwoBitFile...done
Sep 13 04:38:53 Making local copy of GTF file...done
Sep 13 04:38:53 Reading source GTF file...done
Sep 13 04:38:54 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Sep 13 04:38:54 Gene ontology not prepared for this reference
Sep 13 04:38:58 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Sep 13 04:39:03 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
Sep 13 04:39:10 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

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  |                                                                            
  |======================================================================| 100%
done
Sep 13 04:39:12 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
Sep 13 04:39:13 Splice Annotations Filtered
Sep 13 04:39:15 Translating Alternate Splice Peptides...done
Sep 13 04:39:15 Splice Annotations finished

Reference build finished
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
   user  system elapsed 
265.767  28.878 294.603 

Example timings

SpliceWiz.Rcheck/SpliceWiz-Ex.timings

nameusersystemelapsed
ASE-GLM-edgeR2.4710.0952.568
ASE-methods31.575 3.26934.841
ASEFilter-class0.0550.0020.057
Build-Reference-methods56.520 4.06761.331
Coverage3.4360.1161.201
Gene-ontology-methods8.1380.2552.538
Graphics-User-Interface0.0010.0000.000
Mappability-methods2.4020.3222.725
NxtSE-class56.991 3.02560.042
Run_SpliceWiz_Filters8.2500.9869.235
STAR-methods0.0030.0000.005
View-Reference-methods0.1850.0280.213
collateData2.6620.4293.088
coord2GR0.0210.0010.022
covDataObject-class1.7670.1531.917
covPlotObject-class27.412 1.24024.896
covPlotly-class0.9620.0220.977
example-SpliceWiz-data0.0100.0030.013
findSamples0.0040.0010.006
isCOV0.0100.0010.011
makeSE2.0810.3742.454
make_plot_data0.0450.0000.045
plotCoverage16.727 1.12217.684
processBAM2.3840.2851.582
setSWthreads0.0030.0040.004
theme_white0.1720.0350.207