Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:05:20 -0400 (Wed, 12 Apr 2023).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
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 |
To the developers/maintainers of the SpliceWiz package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1945/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpliceWiz 1.0.4 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
Package: SpliceWiz |
Version: 1.0.4 |
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SpliceWiz_1.0.4.tar.gz |
StartedAt: 2023-04-11 00:16:08 -0400 (Tue, 11 Apr 2023) |
EndedAt: 2023-04-11 00:30:33 -0400 (Tue, 11 Apr 2023) |
EllapsedTime: 865.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpliceWiz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings SpliceWiz_1.0.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/SpliceWiz.Rcheck’ * using R version 4.2.3 (2023-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * checking for file ‘SpliceWiz/DESCRIPTION’ ... OK * this is package ‘SpliceWiz’ version ‘1.0.4’ * 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 * checking installed package size ... NOTE installed size is 14.8Mb sub-directories of 1Mb or more: R 1.9Mb libs 11.9Mb * 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 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 NxtSE-class 45.191 0.498 45.754 ASE-methods 41.345 0.709 42.120 Build-Reference-methods 15.885 0.104 15.951 plotCoverage 8.878 0.132 8.762 Run_SpliceWiz_Filters 6.753 0.056 6.810 * 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: 2 NOTEs See ‘/home/biocbuild/bbs-3.16-bioc/meat/SpliceWiz.Rcheck/00check.log’ for details.
SpliceWiz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL SpliceWiz ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-library’ * installing *source* package ‘SpliceWiz’ ... ** using staged installation ** libs g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/ompBAM/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.16-bioc/R/site-library/zlibbioc/include' -I'/home/biocbuild/bbs-3.16-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-3.16-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-3.16-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.16-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 4.2.3 (2023-03-15) -- "Shortstop Beagle" 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 Apr 11 00:23:34 Converting FASTA to local TwoBitFile...done Apr 11 00:23:35 Connecting to genome TwoBitFile...done Apr 11 00:23:35 Making local copy of GTF file...done Apr 11 00:23:35 Extracting temp genome FASTA from TwoBit file Apr 11 00:23:35 Generating synthetic reads, saving to /tmp/Rtmpqdksqn/refWithMapExcl/Mappability/Reads.fa 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 10145 synthetic reads generated Apr 11 00:23:35 Cleaning temp genome / gene annotation files ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.12.3 //================================= setting ==================================\\ || || || Index name : reference_index || || Index space : base space || || Index split : no-split || || Repeat threshold : 100 repeats || || Gapped index : no || || || || Free / total memory : 85.0GB / 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=44.9k bps/s || || 16%, 0 mins elapsed, rate=88.9k bps/s || || 24%, 0 mins elapsed, rate=132.2k bps/s || || 33%, 0 mins elapsed, rate=174.7k bps/s || || 41%, 0 mins elapsed, rate=216.7k bps/s || || 49%, 0 mins elapsed, rate=258.0k bps/s || || 58%, 0 mins elapsed, rate=298.6k bps/s || || 66%, 0 mins elapsed, rate=338.6k bps/s || || 74%, 0 mins elapsed, rate=378.1k bps/s || || 83%, 0 mins elapsed, rate=417.1k bps/s || || 91%, 0 mins elapsed, rate=455.3k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=4.7k bps/s || || 16%, 0 mins elapsed, rate=9.3k bps/s || || 24%, 0 mins elapsed, rate=14.0k bps/s || || 33%, 0 mins elapsed, rate=18.6k bps/s || || 41%, 0 mins elapsed, rate=23.2k bps/s || || 49%, 0 mins elapsed, rate=27.8k bps/s || || 58%, 0 mins elapsed, rate=32.3k bps/s || || 66%, 0 mins elapsed, rate=36.8k bps/s || || 74%, 0 mins elapsed, rate=41.4k bps/s || || 83%, 0 mins elapsed, rate=45.9k bps/s || || 91%, 0 mins elapsed, rate=50.3k 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 2.12.3 //================================= 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 (11-Apr-2023 00:23:45, pid=1207139) ================\\ || || || 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=37.7k 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 11 00:24:15 Calculating Mappability Exclusion regions from: /tmp/Rtmpqdksqn/refWithMapExcl/Mappability/AlignedReads.bam Calculating Mappability Exclusions: /tmp/Rtmpqdksqn/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 11 00:24:18 Reference generated without non-polyA reference Apr 11 00:24:18 Reference generated without Mappability reference Apr 11 00:24:18 Reference generated without Blacklist exclusion Apr 11 00:24:18 Converting FASTA to local TwoBitFile...done Apr 11 00:24:19 Connecting to genome TwoBitFile...done Apr 11 00:24:19 Making local copy of GTF file...done Apr 11 00:24:19 Reading source GTF file...done Apr 11 00:24:19 Processing gtf file... ...genes ...transcripts ...CDS ...exons done Apr 11 00:24:21 Processing introns... ...data ...basic annotations ...splice motifs ...other info ...defining flanking exon clusters done Apr 11 00:24:25 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 11 00:24:32 Predicting NMD transcripts from genome sequence ...exonic transcripts ...retained introns | | | 0% | |======================================================================| 100% done Apr 11 00:24:34 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 11 00:24:35 Splice Annotations Filtered Apr 11 00:24:35 Translating Alternate Splice Peptides...done Apr 11 00:24:36 Splice Annotations finished Reference build finished Apr 11 00:24:36 Running SpliceWiz processBAM Reading reference file Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) Processing BAM file /tmp/Rtmpqdksqn/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/Rtmpqdksqn/02H003.bam processed (412 milliseconds) Apr 11 00:24:36 Running SpliceWiz processBAM Reading reference file Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) Processing BAM file /tmp/Rtmpqdksqn/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/Rtmpqdksqn/02H003.bam processed (287 milliseconds) Apr 11 00:24:37 SpliceWiz reference already exists in given directory Apr 11 00:24:37 Running SpliceWiz processBAM Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /tmp/Rtmpqdksqn/02H003.bam processed (404 milliseconds) /tmp/Rtmpqdksqn/02H025.bam processed (320 milliseconds) /tmp/Rtmpqdksqn/02H026.bam processed (508 milliseconds) /tmp/Rtmpqdksqn/02H033.bam processed (536 milliseconds) /tmp/Rtmpqdksqn/02H043.bam processed (324 milliseconds) /tmp/Rtmpqdksqn/02H046.bam processed (482 milliseconds) Apr 11 00:24:39 Using MulticoreParam 1 threads Apr 11 00:24:39 Validating Experiment; checking COV files... Apr 11 00:24:39 Compiling Sample Stats Apr 11 00:24:39 Compiling Junction List...merging...done Apr 11 00:24:40 Compiling Junction Stats...merging...done Apr 11 00:24:47 Compiling Intron Retention List...done Apr 11 00:24:49 Compiling Tandem Junction List...merging...done Apr 11 00:24:50 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...looking for novel exons Apr 11 00:24:53 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 11 00:25:03 Tidying up splice junctions and intron retentions (part 2)... ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Apr 11 00:25:10 Generating NxtSE assays Apr 11 00:25:10 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Apr 11 00:25:25 Building Final NxtSE Object Apr 11 00:25:27 SpliceWiz (NxtSE) Collation Finished Apr 11 00:25:27 Loading NxtSE object from file...done Apr 11 00:25:28 Removing overlapping introns... Apr 11 00:25:28 Iterating through IR events to determine introns of main isoforms Apr 11 00:25:29 Iteration 1 Apr 11 00:25:30 Iteration 2 Apr 11 00:25:32 SpliceWiz reference already exists in given directory Apr 11 00:25:32 processBAM has already been run on given BAM files Apr 11 00:25:32 Using MulticoreParam 1 threads Apr 11 00:25:32 Validating Experiment; checking COV files... Apr 11 00:25:32 Compiling Sample Stats Apr 11 00:25:32 Compiling Junction List...merging...done Apr 11 00:25:34 Compiling Junction Stats...merging...done Apr 11 00:25:40 Compiling Intron Retention List...done Apr 11 00:25:41 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Apr 11 00:25:50 Generating NxtSE assays Apr 11 00:25:50 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Apr 11 00:26:02 Building Final NxtSE Object Apr 11 00:26:05 SpliceWiz (NxtSE) Collation Finished Apr 11 00:26:05 Loading NxtSE object from file...done Apr 11 00:26:05 Removing overlapping introns... Apr 11 00:26:05 Iterating through IR events to determine introns of main isoforms Apr 11 00:26:06 Iteration 1 Apr 11 00:26:07 Iteration 2 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ] > > # bump to trigger r cmd check > > proc.time() user system elapsed 153.670 15.456 168.989
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
name | user | system | elapsed | |
ASE-methods | 41.345 | 0.709 | 42.120 | |
ASEFilter-class | 0.044 | 0.000 | 0.045 | |
Build-Reference-methods | 15.885 | 0.104 | 15.951 | |
Coverage | 0.825 | 0.020 | 0.821 | |
Graphics-User-Interface | 0 | 0 | 0 | |
Mappability-methods | 1.092 | 0.032 | 1.124 | |
NxtSE-class | 45.191 | 0.498 | 45.754 | |
Run_SpliceWiz_Filters | 6.753 | 0.056 | 6.810 | |
STAR-methods | 0.001 | 0.001 | 0.003 | |
View-Reference-methods | 0.006 | 0.000 | 0.006 | |
collateData | 0.072 | 0.026 | 0.093 | |
coord2GR | 0.016 | 0.000 | 0.016 | |
example-SpliceWiz-data | 0.007 | 0.000 | 0.007 | |
findSamples | 0.005 | 0.000 | 0.005 | |
isCOV | 0.006 | 0.000 | 0.007 | |
makeSE | 4.803 | 0.032 | 4.830 | |
make_plot_data | 3.931 | 0.004 | 3.935 | |
plotCoverage | 8.878 | 0.132 | 8.762 | |
processBAM | 2.553 | 0.194 | 1.585 | |
setSWthreads | 0.007 | 0.004 | 0.028 | |
theme_white | 0.144 | 0.000 | 0.144 | |