| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:25 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 2030/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.4.1 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
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: 1.4.1 |
| 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: 2024-04-16 04:19:11 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 04:42:03 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 1372.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### 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 4.3.3 (2024-02-29)
* 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 22.04.4 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 67.624 2.868 71.258
NxtSE-class 48.298 2.257 50.643
ASE-methods 29.011 1.616 30.661
covPlotObject-class 19.593 0.944 20.348
plotCoverage 12.645 0.236 12.790
Run_SpliceWiz_Filters 7.618 1.080 8.698
* 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
OK
* 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/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)
SpliceWiz.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-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
Apr 16 04:28:44 Converting FASTA to local TwoBitFile...done
Apr 16 04:28:45 Connecting to genome TwoBitFile...done
Apr 16 04:28:45 Making local copy of GTF file...done
Apr 16 04:28:45 Extracting temp genome FASTA from TwoBit file
Apr 16 04:28:46 Generating synthetic reads, saving to /tmp/Rtmpn1hqPd/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Apr 16 04:28:46 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 : 94.2GB / 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=43.3k bps/s ||
|| 16%, 0 mins elapsed, rate=85.8k bps/s ||
|| 24%, 0 mins elapsed, rate=127.6k bps/s ||
|| 33%, 0 mins elapsed, rate=168.6k bps/s ||
|| 41%, 0 mins elapsed, rate=209.1k bps/s ||
|| 49%, 0 mins elapsed, rate=249.1k bps/s ||
|| 58%, 0 mins elapsed, rate=288.3k bps/s ||
|| 66%, 0 mins elapsed, rate=326.9k bps/s ||
|| 74%, 0 mins elapsed, rate=365.1k bps/s ||
|| 83%, 0 mins elapsed, rate=402.8k bps/s ||
|| 91%, 0 mins elapsed, rate=439.9k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=4.2k bps/s ||
|| 16%, 0 mins elapsed, rate=8.4k bps/s ||
|| 24%, 0 mins elapsed, rate=12.6k bps/s ||
|| 33%, 0 mins elapsed, rate=16.7k bps/s ||
|| 41%, 0 mins elapsed, rate=20.9k bps/s ||
|| 49%, 0 mins elapsed, rate=25.0k bps/s ||
|| 58%, 0 mins elapsed, rate=29.1k bps/s ||
|| 66%, 0 mins elapsed, rate=33.1k bps/s ||
|| 74%, 0 mins elapsed, rate=37.2k bps/s ||
|| 83%, 0 mins elapsed, rate=41.3k bps/s ||
|| 91%, 0 mins elapsed, rate=45.3k 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 (16-Apr-2024 04:28:56, pid=3005777) ================\\
|| ||
|| 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=32.9k 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 ||
|| ||
\\============================================================================//
Apr 16 04:29:28 Calculating Mappability Exclusion regions from: /tmp/Rtmpn1hqPd/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /tmp/Rtmpn1hqPd/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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Apr 16 04:29:31 Reference generated without non-polyA reference
Apr 16 04:29:31 Reference generated without Mappability reference
Apr 16 04:29:31 Reference generated without Blacklist exclusion
Apr 16 04:29:31 Converting FASTA to local TwoBitFile...done
Apr 16 04:29:32 Connecting to genome TwoBitFile...done
Apr 16 04:29:32 Making local copy of GTF file...done
Apr 16 04:29:32 Reading source GTF file...done
Apr 16 04:29:33 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 16 04:29:33 Gene ontology not prepared for this reference
Apr 16 04:29:36 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 16 04:29:39 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Apr 16 04:29:46 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Apr 16 04:29:48 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Apr 16 04:29:49 Splice Annotations Filtered
Apr 16 04:29:50 Translating Alternate Splice Peptides...done
Apr 16 04:29:50 Splice Annotations finished
Reference build finished
Apr 16 04:29:51 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/Rtmpn1hqPd/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/Rtmpn1hqPd/02H003.bam processed (402 milliseconds)
Apr 16 04:29:52 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/Rtmpn1hqPd/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/Rtmpn1hqPd/02H003.bam processed (250 milliseconds)
Apr 16 04:29:52 Reference generated without non-polyA reference
Apr 16 04:29:52 Reference generated without Mappability reference
Apr 16 04:29:52 Reference generated without Blacklist exclusion
Apr 16 04:29:52 Converting FASTA to local TwoBitFile...done
Apr 16 04:29:53 Connecting to genome TwoBitFile...done
Apr 16 04:29:53 Making local copy of GTF file...done
Apr 16 04:29:54 Reading source GTF file...done
Apr 16 04:29:54 Processing gtf file...
...genes
...transcripts
...CDS
Apr 16 04:29:54 No protein information detected in reference! For full functionality, ensure there are valid entries with type == `CDS` in the gtf file. Protein reference and NMD annotation is skipped.
...exons
done
Apr 16 04:29:55 Gene ontology not prepared for this reference
Apr 16 04:29:57 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 16 04:30:02 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Apr 16 04:30:09 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Apr 16 04:30:11 Splice Annotations Filtered
Reference build finished
Apr 16 04:30:13 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmpn1hqPd/02H003.bam processed (404 milliseconds)
/tmp/Rtmpn1hqPd/02H025.bam processed (317 milliseconds)
/tmp/Rtmpn1hqPd/02H026.bam processed (501 milliseconds)
/tmp/Rtmpn1hqPd/02H033.bam processed (494 milliseconds)
/tmp/Rtmpn1hqPd/02H043.bam processed (309 milliseconds)
/tmp/Rtmpn1hqPd/02H046.bam processed (452 milliseconds)
Apr 16 04:30:17 Using MulticoreParam 1 threads
Apr 16 04:30:17 Validating Experiment; checking COV files...
Apr 16 04:30:17 Compiling Sample Stats
Apr 16 04:30:17 Compiling Junction List...merging...done
Apr 16 04:30:18 Compiling Junction Stats...merging...done
Apr 16 04:30:26 Compiling Intron Retention List...done
Apr 16 04:30:27 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 16 04:30:37 Generating NxtSE assays
Apr 16 04:30:38 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Apr 16 04:30:52 Building Final NxtSE Object
Apr 16 04:30:52 ...consolidating assays to H5 file
Apr 16 04:30:54 ...packaging reference
Apr 16 04:30:54 ...synthesising NxtSE
Apr 16 04:30:54 ...determining how overlapping introns should be removed
Apr 16 04:30:56 SpliceWiz (NxtSE) Collation Finished
Apr 16 04:30:56 Loading NxtSE object from file...
Apr 16 04:30:56 ...loading reference (NxtSE)
Apr 16 04:30:56 ...linking assays
Apr 16 04:30:56 ...linking COV files
Apr 16 04:30:56 ...loading rowData
Apr 16 04:30:56 ...removing overlapping introns...
Apr 16 04:30:56 NxtSE loaded
Apr 16 04:30:57 SpliceWiz reference already exists in given directory
Apr 16 04:30:57 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmpn1hqPd/02H003.bam processed (400 milliseconds)
/tmp/Rtmpn1hqPd/02H025.bam processed (316 milliseconds)
/tmp/Rtmpn1hqPd/02H026.bam processed (503 milliseconds)
/tmp/Rtmpn1hqPd/02H033.bam processed (507 milliseconds)
/tmp/Rtmpn1hqPd/02H043.bam processed (306 milliseconds)
/tmp/Rtmpn1hqPd/02H046.bam processed (461 milliseconds)
Apr 16 04:31:01 Using MulticoreParam 1 threads
Apr 16 04:31:01 Validating Experiment; checking COV files...
Apr 16 04:31:01 Compiling Sample Stats
Apr 16 04:31:01 Compiling Junction List...merging...done
Apr 16 04:31:02 Compiling Junction Stats...merging...done
Apr 16 04:31:21 Compiling Intron Retention List...done
Apr 16 04:31:22 Compiling Tandem Junction List...merging...done
Apr 16 04:31:23 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Apr 16 04:31:27 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Apr 16 04:31:37 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 16 04:31:46 Generating NxtSE assays
Apr 16 04:31:47 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Apr 16 04:32:02 Building Final NxtSE Object
Apr 16 04:32:02 ...consolidating assays to H5 file
Apr 16 04:32:04 ...packaging reference
Apr 16 04:32:04 ...synthesising NxtSE
Apr 16 04:32:04 ...determining how overlapping introns should be removed
Apr 16 04:32:06 SpliceWiz (NxtSE) Collation Finished
Apr 16 04:32:06 Loading NxtSE object from file...
Apr 16 04:32:06 ...loading reference (NxtSE)
Apr 16 04:32:06 ...linking assays
Apr 16 04:32:07 ...linking COV files
Apr 16 04:32:07 ...loading rowData
Apr 16 04:32:07 ...removing overlapping introns...
Apr 16 04:32:07 NxtSE loaded
Apr 16 04:32:07 SpliceWiz reference already exists in given directory
Apr 16 04:32:07 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/Rtmpn1hqPd/02H003.bam processed (414 milliseconds)
/tmp/Rtmpn1hqPd/02H025.bam processed (332 milliseconds)
/tmp/Rtmpn1hqPd/02H026.bam processed (509 milliseconds)
/tmp/Rtmpn1hqPd/02H033.bam processed (511 milliseconds)
/tmp/Rtmpn1hqPd/02H043.bam processed (319 milliseconds)
/tmp/Rtmpn1hqPd/02H046.bam processed (465 milliseconds)
Apr 16 04:32:11 Using MulticoreParam 1 threads
Apr 16 04:32:11 Validating Experiment; checking COV files...
Apr 16 04:32:11 Compiling Sample Stats
Apr 16 04:32:11 Compiling Junction List...merging...done
Apr 16 04:32:13 Compiling Junction Stats...merging...done
Apr 16 04:32:20 Compiling Intron Retention List...done
Apr 16 04:32:21 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 16 04:32:32 Generating NxtSE assays
Apr 16 04:32:33 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Apr 16 04:32:49 Building Final NxtSE Object
Apr 16 04:32:49 ...consolidating assays to H5 file
Apr 16 04:32:51 ...packaging reference
Apr 16 04:32:51 ...synthesising NxtSE
Apr 16 04:32:51 ...determining how overlapping introns should be removed
Apr 16 04:32:53 SpliceWiz (NxtSE) Collation Finished
Apr 16 04:32:53 Loading NxtSE object from file...
Apr 16 04:32:53 ...loading reference (NxtSE)
Apr 16 04:32:53 ...linking assays
Apr 16 04:32:53 ...linking COV files
Apr 16 04:32:53 ...loading rowData
Apr 16 04:32:53 ...removing overlapping introns...
Apr 16 04:32:53 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
236.260 28.708 265.264
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 3.494 | 0.148 | 3.642 | |
| ASE-methods | 29.011 | 1.616 | 30.661 | |
| ASEFilter-class | 0.042 | 0.000 | 0.043 | |
| Build-Reference-methods | 67.624 | 2.868 | 71.258 | |
| Coverage | 0.863 | 0.023 | 0.881 | |
| Gene-ontology-methods | 1.568 | 0.156 | 1.712 | |
| Graphics-User-Interface | 0.000 | 0.000 | 0.001 | |
| Mappability-methods | 2.604 | 0.452 | 3.055 | |
| NxtSE-class | 48.298 | 2.257 | 50.643 | |
| Run_SpliceWiz_Filters | 7.618 | 1.080 | 8.698 | |
| STAR-methods | 0.005 | 0.000 | 0.005 | |
| View-Reference-methods | 0.151 | 0.020 | 0.171 | |
| collateData | 2.491 | 0.228 | 2.761 | |
| coord2GR | 0.018 | 0.004 | 0.021 | |
| covDataObject-class | 1.524 | 0.052 | 1.573 | |
| covPlotObject-class | 19.593 | 0.944 | 20.348 | |
| covPlotly-class | 0.942 | 0.020 | 0.956 | |
| example-SpliceWiz-data | 0.011 | 0.000 | 0.012 | |
| findSamples | 0.005 | 0.000 | 0.005 | |
| isCOV | 0.012 | 0.000 | 0.011 | |
| makeSE | 1.552 | 0.084 | 1.655 | |
| make_plot_data | 0.045 | 0.000 | 0.045 | |
| plotCoverage | 12.645 | 0.236 | 12.790 | |
| processBAM | 2.455 | 0.208 | 1.543 | |
| setSWthreads | 0.007 | 0.000 | 0.028 | |
| theme_white | 0.116 | 0.004 | 0.120 | |