Alex Chit Hei Wong
| Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/SpliceWiz |
| git_branch: devel |
| git_last_commit: bb75f54 |
| git_last_commit_date: 2024-01-04 21:54:55 -0500 (Thu, 04 Jan 2024) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-04 11:40:00 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4676 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" | 4441 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" | 4417 |
| 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 2012/2251 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.5.2 (landing page) Alex Chit Hei Wong
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
|
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. |
| Package: SpliceWiz |
| Version: 1.5.2 |
| 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_1.5.2.tar.gz |
| StartedAt: 2024-03-02 11:10:37 -0500 (Sat, 02 Mar 2024) |
| EndedAt: 2024-03-02 11:50:05 -0500 (Sat, 02 Mar 2024) |
| EllapsedTime: 2368.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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_1.5.2.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-apple-darwin20
* 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 ‘1.5.2’
* 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 ... 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 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 whether startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files 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 129.569 3.943 174.946
NxtSE-class 70.203 2.095 91.167
ASE-methods 45.564 0.860 52.767
covPlotObject-class 41.357 0.677 49.136
plotCoverage 31.152 0.431 41.377
Run_SpliceWiz_Filters 8.804 0.066 10.439
processBAM 5.990 1.362 5.963
ASE-GLM-edgeR 4.954 0.355 6.035
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceWiz
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-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/4.4-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)
SpliceWiz.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
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
Mar 02 11:31:31 Converting FASTA to local TwoBitFile...done
Mar 02 11:31:33 Connecting to genome TwoBitFile...done
Mar 02 11:31:33 Making local copy of GTF file...done
Mar 02 11:31:33 Extracting temp genome FASTA from TwoBit file
Mar 02 11:31:35 Generating synthetic reads, saving to /private/tmp/Rtmpz5113G/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Mar 02 11:31:35 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.17.1
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 25.0GB / 64.0GB ||
|| ||
|| Input files : 1 file in total ||
|| o genome.fa ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| No format issues were found ||
|| Scan uninformative subreads in reference sequences ... ||
|| Estimate the index size... ||
|| 8%, 0 mins elapsed, rate=19.7k bps/s ||
|| 16%, 0 mins elapsed, rate=38.9k bps/s ||
|| 24%, 0 mins elapsed, rate=57.8k bps/s ||
|| 33%, 0 mins elapsed, rate=76.3k bps/s ||
|| 41%, 0 mins elapsed, rate=94.4k bps/s ||
|| 49%, 0 mins elapsed, rate=112.5k bps/s ||
|| 58%, 0 mins elapsed, rate=130.3k bps/s ||
|| 66%, 0 mins elapsed, rate=147.8k bps/s ||
|| 74%, 0 mins elapsed, rate=165.2k bps/s ||
|| 83%, 0 mins elapsed, rate=182.4k bps/s ||
|| 91%, 0 mins elapsed, rate=198.0k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=2.3k bps/s ||
|| 16%, 0 mins elapsed, rate=4.5k bps/s ||
|| 24%, 0 mins elapsed, rate=6.7k bps/s ||
|| 33%, 0 mins elapsed, rate=9.0k bps/s ||
|| 41%, 0 mins elapsed, rate=11.2k bps/s ||
|| 49%, 0 mins elapsed, rate=13.4k bps/s ||
|| 58%, 0 mins elapsed, rate=15.6k bps/s ||
|| 66%, 0 mins elapsed, rate=17.8k bps/s ||
|| 74%, 0 mins elapsed, rate=20.0k bps/s ||
|| 83%, 0 mins elapsed, rate=22.2k bps/s ||
|| 91%, 0 mins elapsed, rate=24.4k 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 2.17.1
//================================= 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 (02-Mar-2024 11:32:19, pid=51384) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 538 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 65% completed, 11 mins elapsed, rate=15.0k reads per second ||
|| 83% completed, 11 mins elapsed, rate=0.0k reads per second ||
|| 99% completed, 11 mins elapsed, rate=0.0k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 10,145 ||
|| Mapped : 10,145 (100.0%) ||
|| Uniquely mapped : 10,145 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 0 ||
|| ||
|| Junctions : 0 ||
|| Indels : 1 ||
|| ||
|| Running time : 11.9 minutes ||
|| ||
\\============================================================================//
Mar 02 11:44:15 Calculating Mappability Exclusion regions from: /tmp/Rtmpz5113G/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/Rtmpz5113G/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
Mar 02 11:44:24 Reference generated without non-polyA reference
Mar 02 11:44:24 Reference generated without Mappability reference
Mar 02 11:44:24 Reference generated without Blacklist exclusion
Mar 02 11:44:24 Converting FASTA to local TwoBitFile...done
Mar 02 11:44:25 Connecting to genome TwoBitFile...done
Mar 02 11:44:25 Making local copy of GTF file...done
Mar 02 11:44:25 Reading source GTF file...done
Mar 02 11:44:26 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Mar 02 11:44:28 Gene ontology not prepared for this reference
Mar 02 11:44:31 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 02 11:44:38 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
Mar 02 11:44:55 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Mar 02 11:44:59 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 02 11:45:04 Splice Annotations Filtered
Mar 02 11:45:05 Translating Alternate Splice Peptides...done
Mar 02 11:45:07 Splice Annotations finished
Reference build finished
Mar 02 11:45:09 Running SpliceWiz processBAM
Mar 02 11:45:11 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/Rtmpz5113G/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/Rtmpz5113G/02H003.bam processed (1523 milliseconds)
Mar 02 11:45:12 SpliceWiz processBAM processed Rtmpz5113G/02H003.bam
Mar 02 11:45:12 Running SpliceWiz processBAM
Mar 02 11:45:14 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /private/tmp/Rtmpz5113G/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/Rtmpz5113G/02H003.bam processed (884 milliseconds)
Mar 02 11:45:15 SpliceWiz processBAM processed Rtmpz5113G/02H003.bam
Mar 02 11:45:16 Reference generated without non-polyA reference
Mar 02 11:45:16 Reference generated without Mappability reference
Mar 02 11:45:16 Reference generated without Blacklist exclusion
Mar 02 11:45:16 Converting FASTA to local TwoBitFile...done
Mar 02 11:45:17 Connecting to genome TwoBitFile...done
Mar 02 11:45:17 Making local copy of GTF file...done
Mar 02 11:45:18 Reading source GTF file...done
Mar 02 11:45:18 Processing gtf file...
...genes
...transcripts
...CDS
Mar 02 11:45:19 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 02 11:45:21 Gene ontology not prepared for this reference
Mar 02 11:45:24 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 02 11:45:30 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 02 11:45:42 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Mar 02 11:45:44 Splice Annotations Filtered
Reference build finished
Mar 02 11:45:47 Running SpliceWiz processBAM
Mar 02 11:45:48 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H003.bam processed (802 milliseconds)
Mar 02 11:45:49 SpliceWiz processBAM processed Rtmpz5113G/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H025.bam processed (667 milliseconds)
Mar 02 11:45:50 SpliceWiz processBAM processed Rtmpz5113G/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H026.bam processed (1027 milliseconds)
Mar 02 11:45:51 SpliceWiz processBAM processed Rtmpz5113G/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H033.bam processed (994 milliseconds)
Mar 02 11:45:52 SpliceWiz processBAM processed Rtmpz5113G/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H043.bam processed (663 milliseconds)
Mar 02 11:45:52 SpliceWiz processBAM processed Rtmpz5113G/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H046.bam processed (990 milliseconds)
Mar 02 11:45:53 SpliceWiz processBAM processed Rtmpz5113G/02H046.bam
Mar 02 11:45:55 Using MulticoreParam 1 threads
Mar 02 11:45:55 Validating Experiment; checking COV files...
Mar 02 11:45:55 Compiling Sample Stats
Mar 02 11:45:55 Compiling Junction List...merging...done
Mar 02 11:45:57 Compiling Junction Stats...merging...done
Mar 02 11:46:06 Compiling Intron Retention List...done
Mar 02 11:46:08 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 02 11:46:23 Generating NxtSE assays
Mar 02 11:46:25 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Mar 02 11:46:46 Building Final NxtSE Object
Mar 02 11:46:46 ...consolidating assays to H5 file
Mar 02 11:46:50 ...packaging reference
Mar 02 11:46:50 ...synthesising NxtSE
Mar 02 11:46:51 ...determining how overlapping introns should be removed
Mar 02 11:46:56 SpliceWiz (NxtSE) Collation Finished
Mar 02 11:46:56 Loading NxtSE object from file...
Mar 02 11:46:56 ...loading reference (NxtSE)
Mar 02 11:46:56 ...linking assays
Mar 02 11:46:57 ...linking COV files
Mar 02 11:46:57 ...loading rowData
Mar 02 11:46:57 ...removing overlapping introns...
Mar 02 11:46:57 NxtSE loaded
Mar 02 11:47:05 SpliceWiz reference already exists in given directory
Mar 02 11:47:05 Running SpliceWiz processBAM
Mar 02 11:47:06 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H003.bam processed (1106 milliseconds)
Mar 02 11:47:07 SpliceWiz processBAM processed Rtmpz5113G/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H025.bam processed (745 milliseconds)
Mar 02 11:47:08 SpliceWiz processBAM processed Rtmpz5113G/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H026.bam processed (1304 milliseconds)
Mar 02 11:47:10 SpliceWiz processBAM processed Rtmpz5113G/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H033.bam processed (1061 milliseconds)
Mar 02 11:47:11 SpliceWiz processBAM processed Rtmpz5113G/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H043.bam processed (1074 milliseconds)
Mar 02 11:47:12 SpliceWiz processBAM processed Rtmpz5113G/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H046.bam processed (1260 milliseconds)
Mar 02 11:47:13 SpliceWiz processBAM processed Rtmpz5113G/02H046.bam
Mar 02 11:47:14 Using MulticoreParam 1 threads
Mar 02 11:47:14 Validating Experiment; checking COV files...
Mar 02 11:47:14 Compiling Sample Stats
Mar 02 11:47:14 Compiling Junction List...merging...done
Mar 02 11:47:16 Compiling Junction Stats...merging...done
Mar 02 11:47:24 Compiling Intron Retention List...done
Mar 02 11:47:27 Compiling Tandem Junction List...merging...done
Mar 02 11:47:29 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Mar 02 11:47:33 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 02 11:47:51 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Mar 02 11:48:02 Generating NxtSE assays
Mar 02 11:48:04 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Mar 02 11:48:25 Building Final NxtSE Object
Mar 02 11:48:25 ...consolidating assays to H5 file
Mar 02 11:48:27 ...packaging reference
Mar 02 11:48:27 ...synthesising NxtSE
Mar 02 11:48:28 ...determining how overlapping introns should be removed
Mar 02 11:48:32 SpliceWiz (NxtSE) Collation Finished
Mar 02 11:48:32 Loading NxtSE object from file...
Mar 02 11:48:32 ...loading reference (NxtSE)
Mar 02 11:48:32 ...linking assays
Mar 02 11:48:32 ...linking COV files
Mar 02 11:48:32 ...loading rowData
Mar 02 11:48:32 ...removing overlapping introns...
Mar 02 11:48:32 NxtSE loaded
Mar 02 11:48:33 SpliceWiz reference already exists in given directory
Mar 02 11:48:33 Running SpliceWiz processBAM
Mar 02 11:48:35 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H003.bam processed (788 milliseconds)
Mar 02 11:48:35 SpliceWiz processBAM processed Rtmpz5113G/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H025.bam processed (681 milliseconds)
Mar 02 11:48:36 SpliceWiz processBAM processed Rtmpz5113G/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H026.bam processed (969 milliseconds)
Mar 02 11:48:37 SpliceWiz processBAM processed Rtmpz5113G/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H033.bam processed (971 milliseconds)
Mar 02 11:48:38 SpliceWiz processBAM processed Rtmpz5113G/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H043.bam processed (659 milliseconds)
Mar 02 11:48:39 SpliceWiz processBAM processed Rtmpz5113G/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/private/tmp/Rtmpz5113G/02H046.bam processed (886 milliseconds)
Mar 02 11:48:40 SpliceWiz processBAM processed Rtmpz5113G/02H046.bam
Mar 02 11:48:41 Using MulticoreParam 1 threads
Mar 02 11:48:41 Validating Experiment; checking COV files...
Mar 02 11:48:41 Compiling Sample Stats
Mar 02 11:48:41 Compiling Junction List...merging...done
Mar 02 11:48:43 Compiling Junction Stats...merging...done
Mar 02 11:48:52 Compiling Intron Retention List...done
Mar 02 11:48:53 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 02 11:49:08 Generating NxtSE assays
Mar 02 11:49:09 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Mar 02 11:49:30 Building Final NxtSE Object
Mar 02 11:49:30 ...consolidating assays to H5 file
Mar 02 11:49:33 ...packaging reference
Mar 02 11:49:33 ...synthesising NxtSE
Mar 02 11:49:33 ...determining how overlapping introns should be removed
Mar 02 11:49:37 SpliceWiz (NxtSE) Collation Finished
Mar 02 11:49:37 Loading NxtSE object from file...
Mar 02 11:49:37 ...loading reference (NxtSE)
Mar 02 11:49:37 ...linking assays
Mar 02 11:49:38 ...linking COV files
Mar 02 11:49:38 ...loading rowData
Mar 02 11:49:38 ...removing overlapping introns...
Mar 02 11:49:38 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
538.571 359.768 1126.866
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 4.954 | 0.355 | 6.035 | |
| ASE-methods | 45.564 | 0.860 | 52.767 | |
| ASEFilter-class | 0.114 | 0.008 | 0.146 | |
| Build-Reference-methods | 129.569 | 3.943 | 174.946 | |
| Coverage | 1.937 | 0.053 | 2.345 | |
| Gene-ontology-methods | 3.898 | 0.128 | 4.703 | |
| Graphics-User-Interface | 0.001 | 0.001 | 0.001 | |
| Mappability-methods | 2.726 | 0.097 | 3.338 | |
| NxtSE-class | 70.203 | 2.095 | 91.167 | |
| Run_SpliceWiz_Filters | 8.804 | 0.066 | 10.439 | |
| STAR-methods | 0.007 | 0.018 | 0.046 | |
| View-Reference-methods | 0.317 | 0.039 | 0.423 | |
| collateData | 3.223 | 0.102 | 3.854 | |
| coord2GR | 0.046 | 0.003 | 0.064 | |
| covDataObject-class | 3.587 | 0.051 | 4.281 | |
| covPlotObject-class | 41.357 | 0.677 | 49.136 | |
| covPlotly-class | 2.341 | 0.038 | 3.095 | |
| example-SpliceWiz-data | 0.025 | 0.004 | 0.034 | |
| findSamples | 0.012 | 0.009 | 0.026 | |
| isCOV | 0.024 | 0.005 | 0.042 | |
| makeSE | 2.849 | 0.180 | 3.986 | |
| make_plot_data | 0.117 | 0.005 | 0.155 | |
| plotCoverage | 31.152 | 0.431 | 41.377 | |
| processBAM | 5.990 | 1.362 | 5.963 | |
| setSWthreads | 0.005 | 0.015 | 0.025 | |
| theme_white | 0.305 | 0.114 | 0.475 | |