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This page was generated on 2024-03-01 11:36:25 -0500 (Fri, 01 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" 4692
palomino4Windows Server 2022 Datacenterx644.3.2 (2023-10-31 ucrt) -- "Eye Holes" 4445
lconwaymacOS 12.7.1 Montereyx86_644.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" 4466
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: 2024-02-29 14:05:06 -0500 (Thu, 29 Feb 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 -0500 (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
lconwaymacOS 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 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: 1.4.1
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SpliceWiz_1.4.1.tar.gz
StartedAt: 2024-03-01 02:46:09 -0500 (Fri, 01 Mar 2024)
EndedAt: 2024-03-01 03:03:59 -0500 (Fri, 01 Mar 2024)
EllapsedTime: 1069.9 seconds
RetCode: 0
Status:   OK  
CheckDir: SpliceWiz.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings SpliceWiz_1.4.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is 12.6Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    libs   9.2Mb
* 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 loading without being on the library search path ... 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 69.131  2.724  72.666
NxtSE-class             51.143  3.853  55.091
ASE-methods             30.458  1.987  32.468
covPlotObject-class     19.214  0.339  19.374
plotCoverage            12.309  0.060  12.265
Run_SpliceWiz_Filters    6.534  0.264   6.798
* 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 ...
  ‘SW_Cookbook.Rmd’ using ‘UTF-8’... OK
  ‘SW_QuickStart.Rmd’ using ‘UTF-8’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.



Installation output

SpliceWiz.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL SpliceWiz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘SpliceWiz’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c BAM2blocks.cpp -o BAM2blocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c FastaReader.cpp -o FastaReader.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c FragmentBlocks.cpp -o FragmentBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c GZTools.cpp -o GZTools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c covTools.cpp -o covTools.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c main.cpp -o main.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c swEngine.cpp -o swEngine.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.18-bioc/R/site-library/RcppProgress/include' -I/usr/local/include   -fopenmp -DSPLICEWIZ -fpic  -g -O2  -Wall -c synthReadGenerator.cpp -o synthReadGenerator.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.18-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-3.18-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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 2 threads
Use setSWthreads() to set the number of SpliceWiz threads
> 
> test_check("SpliceWiz")
Loading required package: Rsubread
Mar 01 02:55:39 Converting FASTA to local TwoBitFile...done
Mar 01 02:55:40 Connecting to genome TwoBitFile...done
Mar 01 02:55:40 Making local copy of GTF file...done
Mar 01 02:55:40 Extracting temp genome FASTA from TwoBit file
Mar 01 02:55:41 Generating synthetic reads, saving to /tmp/RtmprrhDOu/refWithMapExcl/Mappability/Reads.fa
0%   10   20   30   40   50   60   70   80   90   100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Mar 01 02:55:41 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 : 98.5GB / 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=43.5k bps/s                                  ||
||   16%,   0 mins elapsed, rate=84.8k bps/s                                  ||
||   24%,   0 mins elapsed, rate=124.2k bps/s                                 ||
||   33%,   0 mins elapsed, rate=161.9k bps/s                                 ||
||   41%,   0 mins elapsed, rate=198.2k bps/s                                 ||
||   49%,   0 mins elapsed, rate=233.6k bps/s                                 ||
||   58%,   0 mins elapsed, rate=267.7k bps/s                                 ||
||   66%,   0 mins elapsed, rate=301.2k bps/s                                 ||
||   74%,   0 mins elapsed, rate=334.2k bps/s                                 ||
||   83%,   0 mins elapsed, rate=366.5k bps/s                                 ||
||   91%,   0 mins elapsed, rate=397.7k bps/s                                 ||
|| 3.0 GB of memory is needed for index building.                             ||
|| Build the index...                                                         ||
||    8%,   0 mins elapsed, rate=4.6k bps/s                                   ||
||   16%,   0 mins elapsed, rate=9.1k bps/s                                   ||
||   24%,   0 mins elapsed, rate=13.7k bps/s                                  ||
||   33%,   0 mins elapsed, rate=18.2k bps/s                                  ||
||   41%,   0 mins elapsed, rate=22.7k bps/s                                  ||
||   49%,   0 mins elapsed, rate=27.1k bps/s                                  ||
||   58%,   0 mins elapsed, rate=31.6k bps/s                                  ||
||   66%,   0 mins elapsed, rate=36.0k bps/s                                  ||
||   74%,   0 mins elapsed, rate=40.4k bps/s                                  ||
||   83%,   0 mins elapsed, rate=44.8k bps/s                                  ||
||   91%,   0 mins elapsed, rate=49.2k 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 2.16.1

//================================= 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 (01-Mar-2024 02:55:51, pid=789205) ================\\
||                                                                            ||
|| Check the input reads.                                                     ||
|| The input file contains base space reads.                                  ||
|| Initialise the memory objects.                                             ||
|| Estimate the mean read length.                                             ||
|| Create the output BAM file.                                                ||
|| Check the index.                                                           ||
|| Init the voting space.                                                     ||
|| Load the annotation file.                                                  ||
|| 538 annotation records were loaded.                                        ||
|| Global environment is initialised.                                         ||
|| Load the 1-th index block...                                               ||
|| The index block has been loaded.                                           ||
|| Start read mapping in chunk.                                               ||
||   65% completed, 0.5 mins elapsed, rate=45.7k reads per second             ||
||   83% completed, 0.5 mins elapsed, rate=0.3k reads per second              ||
||   99% completed, 0.5 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 : 0.5 minutes                                  ||
||                                                                            ||
\\============================================================================//

Mar 01 02:56:23 Calculating Mappability Exclusion regions from: /tmp/RtmprrhDOu/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /tmp/RtmprrhDOu/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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Mar 01 02:56:26 Reference generated without non-polyA reference
Mar 01 02:56:26 Reference generated without Mappability reference
Mar 01 02:56:26 Reference generated without Blacklist exclusion
Mar 01 02:56:26 Converting FASTA to local TwoBitFile...done
Mar 01 02:56:27 Connecting to genome TwoBitFile...done
Mar 01 02:56:27 Making local copy of GTF file...done
Mar 01 02:56:27 Reading source GTF file...done
Mar 01 02:56:28 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Mar 01 02:56:29 Gene ontology not prepared for this reference
Mar 01 02:56:31 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 01 02:56:35 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
Mar 01 02:56:41 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns

  |                                                                            
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  |======================================================================| 100%
done
Mar 01 02:56:43 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
Mar 01 02:56:45 Splice Annotations Filtered
Mar 01 02:56:46 Translating Alternate Splice Peptides...done
Mar 01 02:56:46 Splice Annotations finished

Reference build finished
Mar 01 02:56:47 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/RtmprrhDOu/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/RtmprrhDOu/02H003.bam processed (399 milliseconds)
Mar 01 02:56:47 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/RtmprrhDOu/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/RtmprrhDOu/02H003.bam processed (249 milliseconds)
Mar 01 02:56:48 Reference generated without non-polyA reference
Mar 01 02:56:48 Reference generated without Mappability reference
Mar 01 02:56:48 Reference generated without Blacklist exclusion
Mar 01 02:56:48 Converting FASTA to local TwoBitFile...done
Mar 01 02:56:49 Connecting to genome TwoBitFile...done
Mar 01 02:56:49 Making local copy of GTF file...done
Mar 01 02:56:49 Reading source GTF file...done
Mar 01 02:56:49 Processing gtf file...
...genes
...transcripts
...CDS
Mar 01 02:56:50 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
Mar 01 02:56:50 Gene ontology not prepared for this reference
Mar 01 02:56:52 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 01 02:56:56 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
Mar 01 02:57:03 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
Mar 01 02:57:04 Splice Annotations Filtered
Reference build finished
Mar 01 02:57:06 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmprrhDOu/02H003.bam processed (394 milliseconds)
/tmp/RtmprrhDOu/02H025.bam processed (314 milliseconds)
/tmp/RtmprrhDOu/02H026.bam processed (484 milliseconds)
/tmp/RtmprrhDOu/02H033.bam processed (499 milliseconds)
/tmp/RtmprrhDOu/02H043.bam processed (302 milliseconds)
/tmp/RtmprrhDOu/02H046.bam processed (445 milliseconds)
Mar 01 02:57:10 Using MulticoreParam 1 threads
Mar 01 02:57:10 Validating Experiment; checking COV files...
Mar 01 02:57:10 Compiling Sample Stats
Mar 01 02:57:10 Compiling Junction List...merging...done
Mar 01 02:57:11 Compiling Junction Stats...merging...done
Mar 01 02:57:19 Compiling Intron Retention List...done
Mar 01 02:57:20 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Mar 01 02:57:31 Generating NxtSE assays
Mar 01 02:57:32 Using MulticoreParam 1 threads

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

Mar 01 02:57:46 Building Final NxtSE Object
Mar 01 02:57:46 ...consolidating assays to H5 file
Mar 01 02:57:48 ...packaging reference
Mar 01 02:57:48 ...synthesising NxtSE
Mar 01 02:57:48 ...determining how overlapping introns should be removed
Mar 01 02:57:50 SpliceWiz (NxtSE) Collation Finished
Mar 01 02:57:50 Loading NxtSE object from file...
Mar 01 02:57:50 ...loading reference (NxtSE)
Mar 01 02:57:50 ...linking assays
Mar 01 02:57:51 ...linking COV files
Mar 01 02:57:51 ...loading rowData
Mar 01 02:57:51 ...removing overlapping introns...
Mar 01 02:57:51 NxtSE loaded
Mar 01 02:57:51 SpliceWiz reference already exists in given directory
Mar 01 02:57:51 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmprrhDOu/02H003.bam processed (390 milliseconds)
/tmp/RtmprrhDOu/02H025.bam processed (310 milliseconds)
/tmp/RtmprrhDOu/02H026.bam processed (481 milliseconds)
/tmp/RtmprrhDOu/02H033.bam processed (487 milliseconds)
/tmp/RtmprrhDOu/02H043.bam processed (301 milliseconds)
/tmp/RtmprrhDOu/02H046.bam processed (440 milliseconds)
Mar 01 02:57:55 Using MulticoreParam 1 threads
Mar 01 02:57:55 Validating Experiment; checking COV files...
Mar 01 02:57:55 Compiling Sample Stats
Mar 01 02:57:55 Compiling Junction List...merging...done
Mar 01 02:57:56 Compiling Junction Stats...merging...done
Mar 01 02:58:03 Compiling Intron Retention List...done
Mar 01 02:58:04 Compiling Tandem Junction List...merging...done
Mar 01 02:58:05 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Mar 01 02:58:08 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Mar 01 02:58:17 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Mar 01 02:58:25 Generating NxtSE assays
Mar 01 02:58:26 Using MulticoreParam 1 threads

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  |============                                                          |  17%
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  |=======================                                               |  33%
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  |===============================================                       |  67%
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  |==========================================================            |  83%
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Mar 01 02:58:41 Building Final NxtSE Object
Mar 01 02:58:41 ...consolidating assays to H5 file
Mar 01 02:58:42 ...packaging reference
Mar 01 02:58:42 ...synthesising NxtSE
Mar 01 02:58:42 ...determining how overlapping introns should be removed
Mar 01 02:58:45 SpliceWiz (NxtSE) Collation Finished
Mar 01 02:58:45 Loading NxtSE object from file...
Mar 01 02:58:45 ...loading reference (NxtSE)
Mar 01 02:58:45 ...linking assays
Mar 01 02:58:45 ...linking COV files
Mar 01 02:58:45 ...loading rowData
Mar 01 02:58:45 ...removing overlapping introns...
Mar 01 02:58:45 NxtSE loaded
Mar 01 02:58:45 SpliceWiz reference already exists in given directory
Mar 01 02:58:45 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmprrhDOu/02H003.bam processed (400 milliseconds)
/tmp/RtmprrhDOu/02H025.bam processed (314 milliseconds)
/tmp/RtmprrhDOu/02H026.bam processed (488 milliseconds)
/tmp/RtmprrhDOu/02H033.bam processed (495 milliseconds)
/tmp/RtmprrhDOu/02H043.bam processed (303 milliseconds)
/tmp/RtmprrhDOu/02H046.bam processed (488 milliseconds)
Mar 01 02:58:49 Using MulticoreParam 1 threads
Mar 01 02:58:49 Validating Experiment; checking COV files...
Mar 01 02:58:49 Compiling Sample Stats
Mar 01 02:58:49 Compiling Junction List...merging...done
Mar 01 02:58:50 Compiling Junction Stats...merging...done
Mar 01 02:58:58 Compiling Intron Retention List...done
Mar 01 02:58:59 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done

Mar 01 02:59:09 Generating NxtSE assays
Mar 01 02:59:10 Using MulticoreParam 1 threads

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  |=======================                                               |  33%
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  |===================================                                   |  50%
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  |===============================================                       |  67%
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  |==========================================================            |  83%
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  |======================================================================| 100%

Mar 01 02:59:25 Building Final NxtSE Object
Mar 01 02:59:25 ...consolidating assays to H5 file
Mar 01 02:59:26 ...packaging reference
Mar 01 02:59:26 ...synthesising NxtSE
Mar 01 02:59:26 ...determining how overlapping introns should be removed
Mar 01 02:59:28 SpliceWiz (NxtSE) Collation Finished
Mar 01 02:59:28 Loading NxtSE object from file...
Mar 01 02:59:28 ...loading reference (NxtSE)
Mar 01 02:59:28 ...linking assays
Mar 01 02:59:29 ...linking COV files
Mar 01 02:59:29 ...loading rowData
Mar 01 02:59:29 ...removing overlapping introns...
Mar 01 02:59:29 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
> 
> # bump to trigger r cmd check
> 
> proc.time()
   user  system elapsed 
224.793  20.846 245.856 

Example timings

SpliceWiz.Rcheck/SpliceWiz-Ex.timings

nameusersystemelapsed
ASE-GLM-edgeR2.5260.2552.782
ASE-methods30.458 1.98732.468
ASEFilter-class0.0440.0000.044
Build-Reference-methods69.131 2.72472.666
Coverage0.8170.0360.845
Gene-ontology-methods1.5870.1521.726
Graphics-User-Interface000
Mappability-methods2.7060.4363.143
NxtSE-class51.143 3.85355.091
Run_SpliceWiz_Filters6.5340.2646.798
STAR-methods0.0020.0010.004
View-Reference-methods0.1400.0120.152
collateData2.2210.1372.396
coord2GR0.0210.0000.021
covDataObject-class1.4320.0401.469
covPlotObject-class19.214 0.33919.374
covPlotly-class0.9210.0050.919
example-SpliceWiz-data0.0120.0000.011
findSamples0.0010.0030.005
isCOV0.0100.0010.011
makeSE1.6460.0551.722
make_plot_data0.0430.0000.044
plotCoverage12.309 0.06012.265
processBAM2.4970.2081.573
setSWthreads0.0050.0000.020
theme_white0.1230.0040.126