| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:36:25 -0400 (Fri, 29 Mar 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" | 4669 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
| 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: 2024-03-28 03:03:48 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 03:22:00 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 1092.3 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 68.318 2.925 72.042
NxtSE-class 50.111 3.988 54.206
ASE-methods 29.305 1.886 31.232
covPlotObject-class 19.345 1.443 20.568
plotCoverage 12.800 0.897 13.575
Run_SpliceWiz_Filters 6.954 0.840 7.794
* 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 4.3.3 (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
Mar 28 03:13:20 Converting FASTA to local TwoBitFile...done
Mar 28 03:13:21 Connecting to genome TwoBitFile...done
Mar 28 03:13:21 Making local copy of GTF file...done
Mar 28 03:13:21 Extracting temp genome FASTA from TwoBit file
Mar 28 03:13:23 Generating synthetic reads, saving to /tmp/RtmpaYPPFv/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Mar 28 03:13:23 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 : 97.5GB / 125.4GB ||
|| ||
|| Input files : 1 file in total ||
|| o genome.fa ||
|| ||
\\============================================================================//
//================================= Running ==================================\\
|| ||
|| Check the integrity of provided reference sequences ... ||
|| No format issues were found ||
|| Scan uninformative subreads in reference sequences ... ||
|| Estimate the index size... ||
|| 8%, 0 mins elapsed, rate=45.4k bps/s ||
|| 16%, 0 mins elapsed, rate=89.9k bps/s ||
|| 24%, 0 mins elapsed, rate=133.6k bps/s ||
|| 33%, 0 mins elapsed, rate=176.4k bps/s ||
|| 41%, 0 mins elapsed, rate=218.4k bps/s ||
|| 49%, 0 mins elapsed, rate=259.9k bps/s ||
|| 58%, 0 mins elapsed, rate=299.9k bps/s ||
|| 66%, 0 mins elapsed, rate=339.2k bps/s ||
|| 74%, 0 mins elapsed, rate=378.3k bps/s ||
|| 83%, 0 mins elapsed, rate=417.0k bps/s ||
|| 91%, 0 mins elapsed, rate=455.2k 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=33.2k bps/s ||
|| 74%, 0 mins elapsed, rate=37.3k 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 (28-Mar-2024 03:13:33, pid=1397895) ================\\
|| ||
|| 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=33.5k reads per second ||
|| 83% completed, 0.5 mins elapsed, rate=0.3k reads per second ||
|| 99% completed, 0.5 mins elapsed, rate=0.3k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 10,145 ||
|| Mapped : 10,145 (100.0%) ||
|| Uniquely mapped : 10,145 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 0 ||
|| ||
|| Junctions : 0 ||
|| Indels : 1 ||
|| ||
|| Running time : 0.5 minutes ||
|| ||
\\============================================================================//
Mar 28 03:14:04 Calculating Mappability Exclusion regions from: /tmp/RtmpaYPPFv/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /tmp/RtmpaYPPFv/refWithMapExcl/Mappability/AlignedReads.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing Mappability Exclusions
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Mar 28 03:14:08 Reference generated without non-polyA reference
Mar 28 03:14:08 Reference generated without Mappability reference
Mar 28 03:14:08 Reference generated without Blacklist exclusion
Mar 28 03:14:08 Converting FASTA to local TwoBitFile...done
Mar 28 03:14:09 Connecting to genome TwoBitFile...done
Mar 28 03:14:09 Making local copy of GTF file...done
Mar 28 03:14:09 Reading source GTF file...done
Mar 28 03:14:09 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Mar 28 03:14:10 Gene ontology not prepared for this reference
Mar 28 03:14:12 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 28 03:14:21 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Mar 28 03:14:31 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Mar 28 03:14:33 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Mar 28 03:14:34 Splice Annotations Filtered
Mar 28 03:14:35 Translating Alternate Splice Peptides...done
Mar 28 03:14:35 Splice Annotations finished
Reference build finished
Mar 28 03:14:36 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /tmp/RtmpaYPPFv/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/RtmpaYPPFv/02H003.bam processed (422 milliseconds)
Mar 28 03:14:37 Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file /tmp/RtmpaYPPFv/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/RtmpaYPPFv/02H003.bam processed (249 milliseconds)
Mar 28 03:14:37 Reference generated without non-polyA reference
Mar 28 03:14:37 Reference generated without Mappability reference
Mar 28 03:14:37 Reference generated without Blacklist exclusion
Mar 28 03:14:37 Converting FASTA to local TwoBitFile...done
Mar 28 03:14:38 Connecting to genome TwoBitFile...done
Mar 28 03:14:38 Making local copy of GTF file...done
Mar 28 03:14:38 Reading source GTF file...done
Mar 28 03:14:39 Processing gtf file...
...genes
...transcripts
...CDS
Mar 28 03:14:39 No protein information detected in reference! For full functionality, ensure there are valid entries with type == `CDS` in the gtf file. Protein reference and NMD annotation is skipped.
...exons
done
Mar 28 03:14:39 Gene ontology not prepared for this reference
Mar 28 03:14:42 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 28 03:14:45 Generating processBAM reference
...prepping data
...determining measurable introns (directional)
...determining measurable introns (non-directional)
...writing ref-cover.bed
...writing ref-ROI.bed
...writing ref-read-continues.ref
...writing ref-sj.ref
...writing ref-tj.ref
processBAM reference generated
Mar 28 03:14:51 Annotating Splice Events
Annotating Mutually-Exclusive-Exon Splice Events...done
Annotating Skipped-Exon Splice Events...done
Annotating Alternate 5' / 3' Splice Site Splice Events...done
Annotating Alternate First / Last Exon Splice Events...done
Annotating known retained introns...done
Mar 28 03:14:52 Splice Annotations Filtered
Reference build finished
Mar 28 03:14:55 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmpaYPPFv/02H003.bam processed (399 milliseconds)
/tmp/RtmpaYPPFv/02H025.bam processed (319 milliseconds)
/tmp/RtmpaYPPFv/02H026.bam processed (493 milliseconds)
/tmp/RtmpaYPPFv/02H033.bam processed (495 milliseconds)
/tmp/RtmpaYPPFv/02H043.bam processed (308 milliseconds)
/tmp/RtmpaYPPFv/02H046.bam processed (448 milliseconds)
Mar 28 03:14:58 Using MulticoreParam 1 threads
Mar 28 03:14:58 Validating Experiment; checking COV files...
Mar 28 03:14:58 Compiling Sample Stats
Mar 28 03:14:58 Compiling Junction List...merging...done
Mar 28 03:14:59 Compiling Junction Stats...merging...done
Mar 28 03:15:06 Compiling Intron Retention List...done
Mar 28 03:15:07 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Mar 28 03:15:17 Generating NxtSE assays
Mar 28 03:15:19 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Mar 28 03:15:33 Building Final NxtSE Object
Mar 28 03:15:33 ...consolidating assays to H5 file
Mar 28 03:15:35 ...packaging reference
Mar 28 03:15:35 ...synthesising NxtSE
Mar 28 03:15:35 ...determining how overlapping introns should be removed
Mar 28 03:15:37 SpliceWiz (NxtSE) Collation Finished
Mar 28 03:15:37 Loading NxtSE object from file...
Mar 28 03:15:37 ...loading reference (NxtSE)
Mar 28 03:15:37 ...linking assays
Mar 28 03:15:38 ...linking COV files
Mar 28 03:15:38 ...loading rowData
Mar 28 03:15:38 ...removing overlapping introns...
Mar 28 03:15:38 NxtSE loaded
Mar 28 03:15:38 SpliceWiz reference already exists in given directory
Mar 28 03:15:38 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmpaYPPFv/02H003.bam processed (407 milliseconds)
/tmp/RtmpaYPPFv/02H025.bam processed (323 milliseconds)
/tmp/RtmpaYPPFv/02H026.bam processed (495 milliseconds)
/tmp/RtmpaYPPFv/02H033.bam processed (504 milliseconds)
/tmp/RtmpaYPPFv/02H043.bam processed (308 milliseconds)
/tmp/RtmpaYPPFv/02H046.bam processed (464 milliseconds)
Mar 28 03:15:42 Using MulticoreParam 1 threads
Mar 28 03:15:42 Validating Experiment; checking COV files...
Mar 28 03:15:42 Compiling Sample Stats
Mar 28 03:15:42 Compiling Junction List...merging...done
Mar 28 03:15:43 Compiling Junction Stats...merging...done
Mar 28 03:15:51 Compiling Intron Retention List...done
Mar 28 03:15:52 Compiling Tandem Junction List...merging...done
Mar 28 03:15:53 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Mar 28 03:15:56 Assembling novel splicing reference:
...loading reference FASTA/GTF
...injecting novel transcripts to GTF
...processing GTF
...processing introns from GTF
...annotating alternative splicing events
done
Mar 28 03:16:05 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Mar 28 03:16:13 Generating NxtSE assays
Mar 28 03:16:14 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Mar 28 03:16:28 Building Final NxtSE Object
Mar 28 03:16:28 ...consolidating assays to H5 file
Mar 28 03:16:30 ...packaging reference
Mar 28 03:16:30 ...synthesising NxtSE
Mar 28 03:16:30 ...determining how overlapping introns should be removed
Mar 28 03:16:32 SpliceWiz (NxtSE) Collation Finished
Mar 28 03:16:32 Loading NxtSE object from file...
Mar 28 03:16:32 ...loading reference (NxtSE)
Mar 28 03:16:32 ...linking assays
Mar 28 03:16:32 ...linking COV files
Mar 28 03:16:32 ...loading rowData
Mar 28 03:16:32 ...removing overlapping introns...
Mar 28 03:16:32 NxtSE loaded
Mar 28 03:16:33 SpliceWiz reference already exists in given directory
Mar 28 03:16:33 Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/tmp/RtmpaYPPFv/02H003.bam processed (394 milliseconds)
/tmp/RtmpaYPPFv/02H025.bam processed (310 milliseconds)
/tmp/RtmpaYPPFv/02H026.bam processed (487 milliseconds)
/tmp/RtmpaYPPFv/02H033.bam processed (488 milliseconds)
/tmp/RtmpaYPPFv/02H043.bam processed (305 milliseconds)
/tmp/RtmpaYPPFv/02H046.bam processed (440 milliseconds)
Mar 28 03:16:36 Using MulticoreParam 1 threads
Mar 28 03:16:36 Validating Experiment; checking COV files...
Mar 28 03:16:36 Compiling Sample Stats
Mar 28 03:16:36 Compiling Junction List...merging...done
Mar 28 03:16:37 Compiling Junction Stats...merging...done
Mar 28 03:16:45 Compiling Intron Retention List...done
Mar 28 03:16:46 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...copying splicing reference
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Mar 28 03:16:56 Generating NxtSE assays
Mar 28 03:16:57 Using MulticoreParam 1 threads
|
| | 0%
|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Mar 28 03:17:12 Building Final NxtSE Object
Mar 28 03:17:12 ...consolidating assays to H5 file
Mar 28 03:17:13 ...packaging reference
Mar 28 03:17:13 ...synthesising NxtSE
Mar 28 03:17:14 ...determining how overlapping introns should be removed
Mar 28 03:17:16 SpliceWiz (NxtSE) Collation Finished
Mar 28 03:17:16 Loading NxtSE object from file...
Mar 28 03:17:16 ...loading reference (NxtSE)
Mar 28 03:17:16 ...linking assays
Mar 28 03:17:16 ...linking COV files
Mar 28 03:17:16 ...loading rowData
Mar 28 03:17:16 ...removing overlapping introns...
Mar 28 03:17:16 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
226.986 23.501 251.526
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 3.491 | 0.096 | 3.588 | |
| ASE-methods | 29.305 | 1.886 | 31.232 | |
| ASEFilter-class | 0.051 | 0.000 | 0.051 | |
| Build-Reference-methods | 68.318 | 2.925 | 72.042 | |
| Coverage | 0.827 | 0.012 | 0.830 | |
| Gene-ontology-methods | 1.564 | 0.124 | 1.675 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 2.515 | 0.452 | 2.968 | |
| NxtSE-class | 50.111 | 3.988 | 54.206 | |
| Run_SpliceWiz_Filters | 6.954 | 0.840 | 7.794 | |
| STAR-methods | 0.003 | 0.001 | 0.004 | |
| View-Reference-methods | 0.159 | 0.007 | 0.168 | |
| collateData | 2.408 | 0.252 | 2.702 | |
| coord2GR | 0.021 | 0.000 | 0.021 | |
| covDataObject-class | 1.463 | 0.116 | 1.575 | |
| covPlotObject-class | 19.345 | 1.443 | 20.568 | |
| covPlotly-class | 0.947 | 0.040 | 0.981 | |
| example-SpliceWiz-data | 0.012 | 0.000 | 0.012 | |
| findSamples | 0.005 | 0.001 | 0.005 | |
| isCOV | 0.012 | 0.000 | 0.012 | |
| makeSE | 1.817 | 0.253 | 2.088 | |
| make_plot_data | 0.04 | 0.01 | 0.05 | |
| plotCoverage | 12.800 | 0.897 | 13.575 | |
| processBAM | 2.553 | 0.231 | 1.645 | |
| setSWthreads | 0.006 | 0.003 | 0.027 | |
| theme_white | 0.114 | 0.029 | 0.143 | |