Alex Chit Hei Wong
| Snapshot Date: 2023-10-23 14:05:08 -0400 (Mon, 23 Oct 2023) |
| git_url: https://git.bioconductor.org/packages/SpliceWiz |
| git_branch: devel |
| git_last_commit: 90d56d5 |
| git_last_commit_date: 2023-10-22 06:34:11 -0400 (Sun, 22 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-10-24 11:41:34 -0400 (Tue, 24 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4724 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts" | 4459 |
| lconway | macOS 12.6.5 Monterey | x86_64 | 4.3.1 Patched (2023-06-17 r84564) -- "Beagle Scouts" | 4473 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4461 |
| 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 2028/2264 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.3.5 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.6.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.3.1 Ventura / arm64 | see weekly results here | ||||||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: SpliceWiz |
| Version: 1.3.5 |
| Command: /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings SpliceWiz_1.3.5.tar.gz |
| StartedAt: 2023-10-24 13:32:59 -0000 (Tue, 24 Oct 2023) |
| EndedAt: 2023-10-24 13:55:16 -0000 (Tue, 24 Oct 2023) |
| EllapsedTime: 1337.1 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R-4.3.1/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/R/R-4.3.1/site-library --timings SpliceWiz_1.3.5.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (GCC) 10.3.1
GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.3.5’
* 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++ (GCC) 10.3.1’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 14.8Mb
sub-directories of 1Mb or more:
R 2.2Mb
libs 11.4Mb
* 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 90.624 2.439 103.446
NxtSE-class 58.611 1.567 60.316
ASE-methods 37.811 1.362 39.247
covPlotObject-class 26.494 0.713 27.238
plotCoverage 17.758 0.127 17.911
Run_SpliceWiz_Filters 8.577 0.495 9.084
* 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.
SpliceWiz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-4.3.1/bin/R CMD INSTALL SpliceWiz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.3.1/site-library’ * installing *source* package ‘SpliceWiz’ ... ** using staged installation ** libs using C++ compiler: ‘g++ (GCC) 10.3.1’ using C++11 g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/include" -DNDEBUG -I'/home/biocbuild/R/R-4.3.1/site-library/ompBAM/include' -I'/home/biocbuild/R/R-4.3.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.3.1/site-library/zlibbioc/include' -I'/home/biocbuild/R/R-4.3.1/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/R/R-4.3.1/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/R/R-4.3.1/lib -lR installing to /home/biocbuild/R/R-4.3.1/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)
SpliceWiz.Rcheck/tests/testthat.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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
Oct 24 13:45:30 Converting FASTA to local TwoBitFile...done
Oct 24 13:45:32 Connecting to genome TwoBitFile...done
Oct 24 13:45:32 Making local copy of GTF file...done
Oct 24 13:45:32 Extracting temp genome FASTA from TwoBit file
Oct 24 13:45:33 Generating synthetic reads, saving to /home/biocbuild/tmp/RtmpzBhqoe/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Oct 24 13:45:33 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.15.5
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 24.6GB / 62.6GB ||
|| ||
|| 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=59.7k bps/s ||
|| 16%, 0 mins elapsed, rate=117.7k bps/s ||
|| 24%, 0 mins elapsed, rate=173.9k bps/s ||
|| 33%, 0 mins elapsed, rate=228.8k bps/s ||
|| 41%, 0 mins elapsed, rate=282.4k bps/s ||
|| 49%, 0 mins elapsed, rate=334.8k bps/s ||
|| 58%, 0 mins elapsed, rate=385.8k bps/s ||
|| 66%, 0 mins elapsed, rate=435.6k bps/s ||
|| 74%, 0 mins elapsed, rate=484.3k bps/s ||
|| 83%, 0 mins elapsed, rate=532.1k bps/s ||
|| 91%, 0 mins elapsed, rate=578.4k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=2.5k bps/s ||
|| 16%, 0 mins elapsed, rate=5.0k bps/s ||
|| 24%, 0 mins elapsed, rate=7.4k bps/s ||
|| 33%, 0 mins elapsed, rate=9.9k bps/s ||
|| 41%, 0 mins elapsed, rate=12.3k bps/s ||
|| 49%, 0 mins elapsed, rate=14.8k bps/s ||
|| 58%, 0 mins elapsed, rate=17.2k bps/s ||
|| 66%, 0 mins elapsed, rate=19.6k bps/s ||
|| 74%, 0 mins elapsed, rate=22.1k bps/s ||
|| 83%, 0 mins elapsed, rate=24.5k bps/s ||
|| 91%, 0 mins elapsed, rate=26.9k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.2 minutes. ||
|| Index ./reference_index was successfully built. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.15.5
//================================= 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 (24-Oct-2023 13:45:47, pid=322968) ================\\
|| ||
|| 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=26.8k 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 : 10,136 (99.9%) ||
|| Uniquely mapped : 10,136 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 9 ||
|| ||
|| Junctions : 0 ||
|| Indels : 1 ||
|| ||
|| Running time : 0.6 minutes ||
|| ||
\\============================================================================//
Oct 24 13:46:25 Calculating Mappability Exclusion regions from: /home/biocbuild/tmp/RtmpzBhqoe/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /home/biocbuild/tmp/RtmpzBhqoe/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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Oct 24 13:46:29 Reference generated without non-polyA reference
Oct 24 13:46:29 Reference generated without Mappability reference
Oct 24 13:46:29 Reference generated without Blacklist exclusion
Oct 24 13:46:29 Converting FASTA to local TwoBitFile...done
Oct 24 13:46:31 Connecting to genome TwoBitFile...done
Oct 24 13:46:31 Making local copy of GTF file...done
Oct 24 13:46:31 Reading source GTF file...done
Oct 24 13:46:31 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Oct 24 13:46:32 Gene ontology not prepared for this reference
Oct 24 13:46:35 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Oct 24 13:46:41 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Oct 24 13:46:50 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Oct 24 13:46:53 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Oct 24 13:46:54 Splice Annotations Filtered
Oct 24 13:46:55 Translating Alternate Splice Peptides...done
Oct 24 13:46:56 Splice Annotations finished
Reference build finished
Oct 24 13:46:57 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /home/biocbuild/tmp/RtmpzBhqoe/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/home/biocbuild/tmp/RtmpzBhqoe/02H003.bam processed (471 milliseconds)
Oct 24 13:46:58 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /home/biocbuild/tmp/RtmpzBhqoe/02H003.bam
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Compiling data from threads
Performing final sort of fragment maps
Writing COV file
**************************************************|
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[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/home/biocbuild/tmp/RtmpzBhqoe/02H003.bam processed (283 milliseconds)
Oct 24 13:46:58 SpliceWiz reference already exists in given directory
Oct 24 13:46:58 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H003.bam processed (458 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H025.bam processed (356 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H026.bam processed (572 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H033.bam processed (561 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H043.bam processed (355 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H046.bam processed (533 milliseconds)
Oct 24 13:47:02 Using MulticoreParam 1 threads
Oct 24 13:47:02 Validating Experiment; checking COV files...
Oct 24 13:47:02 Compiling Sample Stats
Oct 24 13:47:02 Compiling Junction List...merging...done
Oct 24 13:47:04 Compiling Junction Stats...merging...done
Oct 24 13:47:12 Compiling Intron Retention List...done
Oct 24 13:47:14 Compiling Tandem Junction List...merging...done
Oct 24 13:47:15 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Oct 24 13:47:19 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Oct 24 13:47:31 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Oct 24 13:47:41 Generating NxtSE assays
Oct 24 13:47:42 Using MulticoreParam 1 threads
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|======================= | 33%
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|=============================================== | 67%
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|========================================================== | 83%
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|======================================================================| 100%
Oct 24 13:47:59 Building Final NxtSE Object
Oct 24 13:47:59 ...consolidating assays to H5 file
Oct 24 13:48:01 ...packaging reference
Oct 24 13:48:01 ...synthesising NxtSE
Oct 24 13:48:01 ...determining how overlapping introns should be removed
Oct 24 13:48:04 SpliceWiz (NxtSE) Collation Finished
Oct 24 13:48:04 Loading NxtSE object from file...
Oct 24 13:48:04 ...loading reference (NxtSE)
Oct 24 13:48:04 ...linking assays
Oct 24 13:48:05 ...linking COV files
Oct 24 13:48:05 ...loading rowData
Oct 24 13:48:05 ...removing overlapping introns...
Oct 24 13:48:05 NxtSE loaded
Oct 24 13:48:05 SpliceWiz reference already exists in given directory
Oct 24 13:48:05 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H003.bam processed (451 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H025.bam processed (352 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H026.bam processed (564 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H033.bam processed (552 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H043.bam processed (339 milliseconds)
/home/biocbuild/tmp/RtmpzBhqoe/02H046.bam processed (503 milliseconds)
Oct 24 13:48:09 Using MulticoreParam 1 threads
Oct 24 13:48:09 Validating Experiment; checking COV files...
Oct 24 13:48:09 Compiling Sample Stats
Oct 24 13:48:09 Compiling Junction List...merging...done
Oct 24 13:48:11 Compiling Junction Stats...merging...done
Oct 24 13:48:19 Compiling Intron Retention List...done
Oct 24 13:48:20 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Oct 24 13:48:33 Generating NxtSE assays
Oct 24 13:48:34 Using MulticoreParam 1 threads
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|======================= | 33%
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|=================================== | 50%
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|=============================================== | 67%
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|========================================================== | 83%
|
|======================================================================| 100%
Oct 24 13:48:52 Building Final NxtSE Object
Oct 24 13:48:52 ...consolidating assays to H5 file
Oct 24 13:48:54 ...packaging reference
Oct 24 13:48:54 ...synthesising NxtSE
Oct 24 13:48:54 ...determining how overlapping introns should be removed
Oct 24 13:48:57 SpliceWiz (NxtSE) Collation Finished
Oct 24 13:48:57 Loading NxtSE object from file...
Oct 24 13:48:57 ...loading reference (NxtSE)
Oct 24 13:48:57 ...linking assays
Oct 24 13:48:57 ...linking COV files
Oct 24 13:48:57 ...loading rowData
Oct 24 13:48:57 ...removing overlapping introns...
Oct 24 13:48:57 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
200.768 25.058 226.297
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 4.630 | 0.252 | 4.892 | |
| ASE-methods | 37.811 | 1.362 | 39.247 | |
| ASEFilter-class | 0.061 | 0.004 | 0.065 | |
| Build-Reference-methods | 90.624 | 2.439 | 103.446 | |
| Coverage | 1.243 | 0.012 | 1.258 | |
| Gene-ontology-methods | 2.147 | 0.112 | 2.261 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 2.779 | 0.308 | 3.092 | |
| NxtSE-class | 58.611 | 1.567 | 60.316 | |
| Run_SpliceWiz_Filters | 8.577 | 0.495 | 9.084 | |
| STAR-methods | 0.002 | 0.003 | 0.005 | |
| View-Reference-methods | 0.223 | 0.016 | 0.239 | |
| collateData | 3.185 | 0.430 | 3.618 | |
| coord2GR | 0.043 | 0.004 | 0.047 | |
| covDataObject-class | 2.056 | 0.095 | 2.166 | |
| covPlotObject-class | 26.494 | 0.713 | 27.238 | |
| covPlotly-class | 1.635 | 0.006 | 1.643 | |
| example-SpliceWiz-data | 0.021 | 0.004 | 0.025 | |
| findSamples | 0.007 | 0.000 | 0.007 | |
| isCOV | 0.024 | 0.000 | 0.024 | |
| makeSE | 2.172 | 0.107 | 2.280 | |
| make_plot_data | 0.084 | 0.000 | 0.084 | |
| plotCoverage | 17.758 | 0.127 | 17.911 | |
| processBAM | 2.515 | 0.202 | 1.719 | |
| setSWthreads | 0.004 | 0.002 | 0.004 | |
| theme_white | 0.177 | 0.004 | 0.182 | |