| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-11-30 11:36:14 -0500 (Thu, 30 Nov 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4685 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4420 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4439 |
| 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 1.4.0 (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 12.7.1 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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2023-11-30 02:01:31 -0500 (Thu, 30 Nov 2023) |
| EndedAt: 2023-11-30 02:19:26 -0500 (Thu, 30 Nov 2023) |
| EllapsedTime: 1074.8 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.3.2 Patched (2023-11-13 r85521)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpliceWiz’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
installed size is 12.6Mb
sub-directories of 1Mb or more:
R 2.2Mb
libs 9.2Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Build-Reference-methods 69.026 3.654 73.607
NxtSE-class 52.175 2.757 55.031
ASE-methods 29.100 0.469 29.611
covPlotObject-class 18.569 1.044 19.395
plotCoverage 13.105 0.372 13.379
Run_SpliceWiz_Filters 7.367 0.788 8.155
* 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/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 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 2 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Nov 30 02:11:29 Converting FASTA to local TwoBitFile...done
Nov 30 02:11:30 Connecting to genome TwoBitFile...done
Nov 30 02:11:30 Making local copy of GTF file...done
Nov 30 02:11:30 Extracting temp genome FASTA from TwoBit file
Nov 30 02:11:31 Generating synthetic reads, saving to /tmp/RtmprUU0AV/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Nov 30 02:11:31 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.16.0
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 88.2GB / 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=45.2k bps/s ||
|| 16%, 0 mins elapsed, rate=89.5k bps/s ||
|| 24%, 0 mins elapsed, rate=133.0k bps/s ||
|| 33%, 0 mins elapsed, rate=175.7k bps/s ||
|| 41%, 0 mins elapsed, rate=217.7k bps/s ||
|| 49%, 0 mins elapsed, rate=259.1k bps/s ||
|| 58%, 0 mins elapsed, rate=299.6k bps/s ||
|| 66%, 0 mins elapsed, rate=339.3k bps/s ||
|| 74%, 0 mins elapsed, rate=378.4k bps/s ||
|| 83%, 0 mins elapsed, rate=416.8k bps/s ||
|| 91%, 0 mins elapsed, rate=454.7k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=4.1k bps/s ||
|| 16%, 0 mins elapsed, rate=8.3k bps/s ||
|| 24%, 0 mins elapsed, rate=12.4k bps/s ||
|| 33%, 0 mins elapsed, rate=16.5k bps/s ||
|| 41%, 0 mins elapsed, rate=20.5k bps/s ||
|| 49%, 0 mins elapsed, rate=24.6k bps/s ||
|| 58%, 0 mins elapsed, rate=28.6k bps/s ||
|| 66%, 0 mins elapsed, rate=32.6k bps/s ||
|| 74%, 0 mins elapsed, rate=36.6k bps/s ||
|| 83%, 0 mins elapsed, rate=40.6k bps/s ||
|| 91%, 0 mins elapsed, rate=44.6k bps/s ||
|| Save current index block... ||
|| [ 0.0% finished ] ||
|| [ 10.0% finished ] ||
|| [ 20.0% finished ] ||
|| [ 30.0% finished ] ||
|| [ 40.0% finished ] ||
|| [ 50.0% finished ] ||
|| [ 60.0% finished ] ||
|| [ 70.0% finished ] ||
|| [ 80.0% finished ] ||
|| [ 90.0% finished ] ||
|| [ 100.0% finished ] ||
|| ||
|| Total running time: 0.2 minutes. ||
|| Index ./reference_index was successfully built. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.16.0
//================================= 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 (30-Nov-2023 02:11:42, pid=4114374) ================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 538 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 65% completed, 0.5 mins elapsed, rate=45.9k 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 ||
|| ||
\\============================================================================//
Nov 30 02:12:14 Calculating Mappability Exclusion regions from: /tmp/RtmprUU0AV/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /tmp/RtmprUU0AV/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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Nov 30 02:12:17 Reference generated without non-polyA reference
Nov 30 02:12:17 Reference generated without Mappability reference
Nov 30 02:12:17 Reference generated without Blacklist exclusion
Nov 30 02:12:17 Converting FASTA to local TwoBitFile...done
Nov 30 02:12:19 Connecting to genome TwoBitFile...done
Nov 30 02:12:19 Making local copy of GTF file...done
Nov 30 02:12:19 Reading source GTF file...done
Nov 30 02:12:19 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Nov 30 02:12:20 Gene ontology not prepared for this reference
Nov 30 02:12:23 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Nov 30 02:12:26 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
Nov 30 02:12:34 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Nov 30 02:12:37 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
Nov 30 02:12:38 Splice Annotations Filtered
Nov 30 02:12:39 Translating Alternate Splice Peptides...done
Nov 30 02:12:39 Splice Annotations finished
Reference build finished
Nov 30 02:12:41 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/RtmprUU0AV/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/RtmprUU0AV/02H003.bam processed (404 milliseconds)
Nov 30 02:12:41 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/RtmprUU0AV/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/RtmprUU0AV/02H003.bam processed (252 milliseconds)
Nov 30 02:12:41 SpliceWiz reference already exists in given directory
Nov 30 02:12:41 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmprUU0AV/02H003.bam processed (392 milliseconds)
/tmp/RtmprUU0AV/02H025.bam processed (311 milliseconds)
/tmp/RtmprUU0AV/02H026.bam processed (491 milliseconds)
/tmp/RtmprUU0AV/02H033.bam processed (497 milliseconds)
/tmp/RtmprUU0AV/02H043.bam processed (309 milliseconds)
/tmp/RtmprUU0AV/02H046.bam processed (450 milliseconds)
Nov 30 02:12:45 Using MulticoreParam 1 threads
Nov 30 02:12:45 Validating Experiment; checking COV files...
Nov 30 02:12:45 Compiling Sample Stats
Nov 30 02:12:45 Compiling Junction List...merging...done
Nov 30 02:12:46 Compiling Junction Stats...merging...done
Nov 30 02:12:55 Compiling Intron Retention List...done
Nov 30 02:12:56 Compiling Tandem Junction List...merging...done
Nov 30 02:12:57 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Nov 30 02:13:01 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Nov 30 02:13:11 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Nov 30 02:13:20 Generating NxtSE assays
Nov 30 02:13:21 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Nov 30 02:13:37 Building Final NxtSE Object
Nov 30 02:13:37 ...consolidating assays to H5 file
Nov 30 02:13:39 ...packaging reference
Nov 30 02:13:39 ...synthesising NxtSE
Nov 30 02:13:39 ...determining how overlapping introns should be removed
Nov 30 02:13:42 SpliceWiz (NxtSE) Collation Finished
Nov 30 02:13:42 Loading NxtSE object from file...
Nov 30 02:13:42 ...loading reference (NxtSE)
Nov 30 02:13:42 ...linking assays
Nov 30 02:13:42 ...linking COV files
Nov 30 02:13:42 ...loading rowData
Nov 30 02:13:42 ...removing overlapping introns...
Nov 30 02:13:42 NxtSE loaded
Nov 30 02:13:42 SpliceWiz reference already exists in given directory
Nov 30 02:13:42 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmprUU0AV/02H003.bam processed (392 milliseconds)
/tmp/RtmprUU0AV/02H025.bam processed (318 milliseconds)
/tmp/RtmprUU0AV/02H026.bam processed (498 milliseconds)
/tmp/RtmprUU0AV/02H033.bam processed (497 milliseconds)
/tmp/RtmprUU0AV/02H043.bam processed (306 milliseconds)
/tmp/RtmprUU0AV/02H046.bam processed (452 milliseconds)
Nov 30 02:13:46 Using MulticoreParam 1 threads
Nov 30 02:13:46 Validating Experiment; checking COV files...
Nov 30 02:13:46 Compiling Sample Stats
Nov 30 02:13:46 Compiling Junction List...merging...done
Nov 30 02:13:47 Compiling Junction Stats...merging...done
Nov 30 02:13:55 Compiling Intron Retention List...done
Nov 30 02:13:56 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Nov 30 02:14:07 Generating NxtSE assays
Nov 30 02:14:09 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Nov 30 02:14:25 Building Final NxtSE Object
Nov 30 02:14:25 ...consolidating assays to H5 file
Nov 30 02:14:27 ...packaging reference
Nov 30 02:14:27 ...synthesising NxtSE
Nov 30 02:14:27 ...determining how overlapping introns should be removed
Nov 30 02:14:30 SpliceWiz (NxtSE) Collation Finished
Nov 30 02:14:30 Loading NxtSE object from file...
Nov 30 02:14:30 ...loading reference (NxtSE)
Nov 30 02:14:30 ...linking assays
Nov 30 02:14:30 ...linking COV files
Nov 30 02:14:30 ...loading rowData
Nov 30 02:14:30 ...removing overlapping introns...
Nov 30 02:14:30 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
183.366 22.757 208.723
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 3.460 | 0.124 | 3.584 | |
| ASE-methods | 29.100 | 0.469 | 29.611 | |
| ASEFilter-class | 0.045 | 0.000 | 0.045 | |
| Build-Reference-methods | 69.026 | 3.654 | 73.607 | |
| Coverage | 0.808 | 0.016 | 0.818 | |
| Gene-ontology-methods | 1.430 | 0.072 | 1.490 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 2.209 | 0.072 | 2.281 | |
| NxtSE-class | 52.175 | 2.757 | 55.031 | |
| Run_SpliceWiz_Filters | 7.367 | 0.788 | 8.155 | |
| STAR-methods | 0.003 | 0.002 | 0.004 | |
| View-Reference-methods | 0.167 | 0.004 | 0.171 | |
| collateData | 2.692 | 0.425 | 3.150 | |
| coord2GR | 0.021 | 0.000 | 0.021 | |
| covDataObject-class | 1.404 | 0.092 | 1.493 | |
| covPlotObject-class | 18.569 | 1.044 | 19.395 | |
| covPlotly-class | 0.965 | 0.016 | 0.975 | |
| example-SpliceWiz-data | 0.012 | 0.000 | 0.012 | |
| findSamples | 0.005 | 0.000 | 0.006 | |
| isCOV | 0.011 | 0.000 | 0.011 | |
| makeSE | 1.614 | 0.145 | 1.781 | |
| make_plot_data | 0.046 | 0.000 | 0.046 | |
| plotCoverage | 13.105 | 0.372 | 13.379 | |
| processBAM | 2.435 | 0.269 | 1.583 | |
| setSWthreads | 0.005 | 0.001 | 0.025 | |
| theme_white | 0.142 | 0.028 | 0.171 | |