Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-07-09 17:44 -0400 (Tue, 09 Jul 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4709 |
palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2054/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpliceWiz 1.6.0 (landing page) Alex Chit Hei Wong
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the SpliceWiz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceWiz.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SpliceWiz |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.6.0.tar.gz |
StartedAt: 2024-07-09 10:35:28 -0400 (Tue, 09 Jul 2024) |
EndedAt: 2024-07-09 10:57:17 -0400 (Tue, 09 Jul 2024) |
EllapsedTime: 1309.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: SpliceWiz.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpliceWiz/DESCRIPTION’ ... OK * this is package ‘SpliceWiz’ version ‘1.6.0’ * 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: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ * used SDK: ‘MacOSX11.3.sdk’ * checking C++ specification ... NOTE Specified C++11: please drop specification unless essential * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether 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 NxtSE-class 65.611 1.014 67.104 Build-Reference-methods 63.455 1.320 67.524 ASE-methods 35.012 0.282 35.661 covPlotObject-class 21.757 0.449 22.386 plotCoverage 13.769 0.146 14.024 Run_SpliceWiz_Filters 9.468 0.039 9.544 processBAM 4.937 0.653 4.025 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/Users/biocbuild/bbs-3.19-bioc/meat/SpliceWiz.Rcheck/00check.log’ for details.
SpliceWiz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceWiz ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘SpliceWiz’ ... ** using staged installation Configuring without OpenMP for MacOS ** libs using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c BAM2blocks.cpp -o BAM2blocks.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FastaReader.cpp -o FastaReader.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FragmentBlocks.cpp -o FragmentBlocks.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c GZTools.cpp -o GZTools.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_CoverageBlocks.cpp:251:16: warning: variable 'len' set but not used [-Wunused-but-set-variable] unsigned int len=0; ^ 1 warning generated. clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c covTools.cpp -o covTools.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c swEngine.cpp -o swEngine.o clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c synthReadGenerator.cpp -o synthReadGenerator.o clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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 -DSPLICEWIZ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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 1 threads Use setSWthreads() to set the number of SpliceWiz threads > > test_check("SpliceWiz") Loading required package: Rsubread Jul 09 10:46:20 Converting FASTA to local TwoBitFile...done Jul 09 10:46:22 Connecting to genome TwoBitFile...done Jul 09 10:46:22 Making local copy of GTF file...done Jul 09 10:46:22 Extracting temp genome FASTA from TwoBit file Jul 09 10:46:23 Generating synthetic reads, saving to /private/tmp/Rtmp9nN4An/refWithMapExcl/Mappability/Reads.fa 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 10145 synthetic reads generated Jul 09 10:46:23 Cleaning temp genome / gene annotation files ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.18.0 //================================= setting ==================================\\ || || || Index name : reference_index || || Index space : base space || || Index split : no-split || || Repeat threshold : 100 repeats || || Gapped index : no || || || || Free / total memory : 40.5GB / 64.0GB || || || || 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=91.2k bps/s || || 16%, 0 mins elapsed, rate=177.2k bps/s || || 24%, 0 mins elapsed, rate=254.9k bps/s || || 33%, 0 mins elapsed, rate=329.9k bps/s || || 41%, 0 mins elapsed, rate=402.9k bps/s || || 49%, 0 mins elapsed, rate=472.5k bps/s || || 58%, 0 mins elapsed, rate=538.8k bps/s || || 66%, 0 mins elapsed, rate=601.7k bps/s || || 74%, 0 mins elapsed, rate=662.9k bps/s || || 83%, 0 mins elapsed, rate=722.0k bps/s || || 91%, 0 mins elapsed, rate=778.4k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=6.9k bps/s || || 16%, 0 mins elapsed, rate=13.8k bps/s || || 24%, 0 mins elapsed, rate=20.5k bps/s || || 33%, 0 mins elapsed, rate=27.2k bps/s || || 41%, 0 mins elapsed, rate=33.9k bps/s || || 49%, 0 mins elapsed, rate=40.5k bps/s || || 58%, 0 mins elapsed, rate=47.0k bps/s || || 66%, 0 mins elapsed, rate=53.4k bps/s || || 74%, 0 mins elapsed, rate=59.8k bps/s || || 83%, 0 mins elapsed, rate=66.1k bps/s || || 91%, 0 mins elapsed, rate=72.3k 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: 0.3 minutes. || || Index ./reference_index was successfully built. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.18.0 //================================= 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 (09-Jul-2024 10:46:42, pid=18093) =================\\ || || || 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, 6.3 mins elapsed, rate=28.5k reads per second || || 83% completed, 6.3 mins elapsed, rate=0.0k reads per second || || 99% completed, 6.3 mins elapsed, rate=0.0k 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 : 6.3 minutes || || || \\============================================================================// Jul 09 10:52:58 Calculating Mappability Exclusion regions from: /tmp/Rtmp9nN4An/refWithMapExcl/Mappability/AlignedReads.bam Calculating Mappability Exclusions: /private/tmp/Rtmp9nN4An/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% [----|----|----|----|----|----|----|----|----|----| **************************************************| SpliceWiz was compiled without OpenMP Jul 09 10:53:02 Reference generated without non-polyA reference Jul 09 10:53:02 Reference generated without Mappability reference Jul 09 10:53:02 Reference generated without Blacklist exclusion Jul 09 10:53:02 Converting FASTA to local TwoBitFile...done Jul 09 10:53:03 Connecting to genome TwoBitFile...done Jul 09 10:53:03 Making local copy of GTF file...done Jul 09 10:53:03 Reading source GTF file...done Jul 09 10:53:04 Processing gtf file... ...genes ...transcripts ...CDS ...exons done Jul 09 10:53:05 Gene ontology not prepared for this reference Jul 09 10:53:08 Processing introns... ...data ...basic annotations ...splice motifs ...other info ...defining flanking exon clusters done Jul 09 10:53:13 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 Jul 09 10:53:21 Predicting NMD transcripts from genome sequence ...exonic transcripts ...retained introns | | | 0% | |======================================================================| 100% done Jul 09 10:53:24 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 Jul 09 10:53:26 Splice Annotations Filtered Jul 09 10:53:27 Translating Alternate Splice Peptides...done Jul 09 10:53:28 Splice Annotations finished Reference build finished Jul 09 10:53:29 Running SpliceWiz processBAM Jul 09 10:53:30 Using MulticoreParam 1 threads Reading reference file Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) Processing BAM file /private/tmp/Rtmp9nN4An/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 /private/tmp/Rtmp9nN4An/02H003.bam processed (528 milliseconds) Jul 09 10:53:31 SpliceWiz processBAM processed Rtmp9nN4An/02H003.bam Jul 09 10:53:31 Running SpliceWiz processBAM Jul 09 10:53:32 Using MulticoreParam 1 threads Reading reference file Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) Processing BAM file /private/tmp/Rtmp9nN4An/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 /private/tmp/Rtmp9nN4An/02H003.bam processed (521 milliseconds) Jul 09 10:53:33 SpliceWiz processBAM processed Rtmp9nN4An/02H003.bam Jul 09 10:53:33 Reference generated without non-polyA reference Jul 09 10:53:33 Reference generated without Mappability reference Jul 09 10:53:33 Reference generated without Blacklist exclusion Jul 09 10:53:33 Converting FASTA to local TwoBitFile...done Jul 09 10:53:35 Connecting to genome TwoBitFile...done Jul 09 10:53:35 Making local copy of GTF file...done Jul 09 10:53:35 Reading source GTF file...done Jul 09 10:53:35 Processing gtf file... ...genes ...transcripts ...CDS Jul 09 10:53:35 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 Jul 09 10:53:36 Gene ontology not prepared for this reference Jul 09 10:53:38 Processing introns... ...data ...basic annotations ...splice motifs ...other info ...defining flanking exon clusters done Jul 09 10:53:43 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 Jul 09 10:53:51 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 Jul 09 10:53:52 Splice Annotations Filtered Reference build finished Jul 09 10:53:55 Running SpliceWiz processBAM Jul 09 10:53:56 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H003.bam processed (520 milliseconds) Jul 09 10:53:57 SpliceWiz processBAM processed Rtmp9nN4An/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H025.bam processed (431 milliseconds) Jul 09 10:53:57 SpliceWiz processBAM processed Rtmp9nN4An/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H026.bam processed (643 milliseconds) Jul 09 10:53:58 SpliceWiz processBAM processed Rtmp9nN4An/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H033.bam processed (626 milliseconds) Jul 09 10:53:59 SpliceWiz processBAM processed Rtmp9nN4An/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H043.bam processed (411 milliseconds) Jul 09 10:53:59 SpliceWiz processBAM processed Rtmp9nN4An/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H046.bam processed (599 milliseconds) Jul 09 10:54:00 SpliceWiz processBAM processed Rtmp9nN4An/02H046.bam Jul 09 10:54:01 Using MulticoreParam 1 threads Jul 09 10:54:01 Validating Experiment; checking COV files... Jul 09 10:54:01 Compiling Sample Stats Jul 09 10:54:01 Compiling Junction List...merging...done Jul 09 10:54:02 Compiling Junction Stats...merging...done Jul 09 10:54:12 Compiling Intron Retention List...done Jul 09 10:54:13 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...copying splicing reference ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Jul 09 10:54:26 Generating NxtSE assays Jul 09 10:54:27 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Jul 09 10:54:46 Building Final NxtSE Object Jul 09 10:54:46 ...consolidating assays to H5 file Jul 09 10:54:48 ...packaging reference Jul 09 10:54:48 ...synthesising NxtSE Jul 09 10:54:48 ...determining how overlapping introns should be removed Jul 09 10:54:51 SpliceWiz (NxtSE) Collation Finished Jul 09 10:54:51 Loading NxtSE object from file... Jul 09 10:54:51 ...loading reference (NxtSE) Jul 09 10:54:51 ...linking assays Jul 09 10:54:51 ...linking COV files Jul 09 10:54:51 ...loading rowData Jul 09 10:54:51 ...removing overlapping introns... Jul 09 10:54:52 NxtSE loaded Jul 09 10:54:52 SpliceWiz reference already exists in given directory Jul 09 10:54:52 Running SpliceWiz processBAM Jul 09 10:54:53 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H003.bam processed (530 milliseconds) Jul 09 10:54:54 SpliceWiz processBAM processed Rtmp9nN4An/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H025.bam processed (433 milliseconds) Jul 09 10:54:54 SpliceWiz processBAM processed Rtmp9nN4An/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H026.bam processed (632 milliseconds) Jul 09 10:54:55 SpliceWiz processBAM processed Rtmp9nN4An/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H033.bam processed (640 milliseconds) Jul 09 10:54:56 SpliceWiz processBAM processed Rtmp9nN4An/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H043.bam processed (411 milliseconds) Jul 09 10:54:56 SpliceWiz processBAM processed Rtmp9nN4An/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H046.bam processed (597 milliseconds) Jul 09 10:54:57 SpliceWiz processBAM processed Rtmp9nN4An/02H046.bam Jul 09 10:54:58 Using MulticoreParam 1 threads Jul 09 10:54:58 Validating Experiment; checking COV files... Jul 09 10:54:58 Compiling Sample Stats Jul 09 10:54:58 Compiling Junction List...merging...done Jul 09 10:54:59 Compiling Junction Stats...merging...done Jul 09 10:55:09 Compiling Intron Retention List...done Jul 09 10:55:10 Compiling Tandem Junction List...merging...done Jul 09 10:55:12 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...looking for novel exons Jul 09 10:55:16 Assembling novel splicing reference: ...loading reference FASTA/GTF ...injecting novel transcripts to GTF ...processing GTF ...processing introns from GTF ...annotating alternative splicing events done Jul 09 10:55:28 Tidying up splice junctions and intron retentions (part 2)... ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Jul 09 10:55:39 Generating NxtSE assays Jul 09 10:55:40 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Jul 09 10:55:59 Building Final NxtSE Object Jul 09 10:55:59 ...consolidating assays to H5 file Jul 09 10:56:00 ...packaging reference Jul 09 10:56:01 ...synthesising NxtSE Jul 09 10:56:01 ...determining how overlapping introns should be removed Jul 09 10:56:04 SpliceWiz (NxtSE) Collation Finished Jul 09 10:56:04 Loading NxtSE object from file... Jul 09 10:56:04 ...loading reference (NxtSE) Jul 09 10:56:04 ...linking assays Jul 09 10:56:04 ...linking COV files Jul 09 10:56:04 ...loading rowData Jul 09 10:56:04 ...removing overlapping introns... Jul 09 10:56:04 NxtSE loaded Jul 09 10:56:05 SpliceWiz reference already exists in given directory Jul 09 10:56:05 Running SpliceWiz processBAM Jul 09 10:56:06 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H003.bam processed (457 milliseconds) Jul 09 10:56:07 SpliceWiz processBAM processed Rtmp9nN4An/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H025.bam processed (282 milliseconds) Jul 09 10:56:07 SpliceWiz processBAM processed Rtmp9nN4An/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H026.bam processed (426 milliseconds) Jul 09 10:56:07 SpliceWiz processBAM processed Rtmp9nN4An/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H033.bam processed (603 milliseconds) Jul 09 10:56:08 SpliceWiz processBAM processed Rtmp9nN4An/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H043.bam processed (416 milliseconds) Jul 09 10:56:08 SpliceWiz processBAM processed Rtmp9nN4An/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds) /private/tmp/Rtmp9nN4An/02H046.bam processed (599 milliseconds) Jul 09 10:56:09 SpliceWiz processBAM processed Rtmp9nN4An/02H046.bam Jul 09 10:56:10 Using MulticoreParam 1 threads Jul 09 10:56:10 Validating Experiment; checking COV files... Jul 09 10:56:10 Compiling Sample Stats Jul 09 10:56:10 Compiling Junction List...merging...done Jul 09 10:56:12 Compiling Junction Stats...merging...done Jul 09 10:56:21 Compiling Intron Retention List...done Jul 09 10:56:23 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...copying splicing reference ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Jul 09 10:56:36 Generating NxtSE assays Jul 09 10:56:37 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Jul 09 10:56:56 Building Final NxtSE Object Jul 09 10:56:56 ...consolidating assays to H5 file Jul 09 10:56:57 ...packaging reference Jul 09 10:56:57 ...synthesising NxtSE Jul 09 10:56:58 ...determining how overlapping introns should be removed Jul 09 10:57:01 SpliceWiz (NxtSE) Collation Finished Jul 09 10:57:01 Loading NxtSE object from file... Jul 09 10:57:01 ...loading reference (NxtSE) Jul 09 10:57:01 ...linking assays Jul 09 10:57:01 ...linking COV files Jul 09 10:57:01 ...loading rowData Jul 09 10:57:01 ...removing overlapping introns... Jul 09 10:57:01 NxtSE loaded path paired strand depth mean_frag_size 02H003 ../SpliceWiz_Output/02H003.txt.gz TRUE -1 106256 149.3108 02H025 ../SpliceWiz_Output/02H025.txt.gz TRUE -1 84872 151.5914 02H026 ../SpliceWiz_Output/02H026.txt.gz TRUE -1 131514 150.3238 02H033 ../SpliceWiz_Output/02H033.txt.gz TRUE -1 129013 153.9754 02H043 ../SpliceWiz_Output/02H043.txt.gz TRUE -1 80254 155.4004 02H046 ../SpliceWiz_Output/02H046.txt.gz TRUE -1 120174 151.2840 directionality_strength Intergenic_Fraction rRNA_Fraction 02H003 9850 0 0 02H025 9848 0 0 02H026 9848 0 0 02H033 9855 0 0 02H043 9841 0 0 02H046 9857 0 0 NonPolyA_Fraction Mitochondrial_Fraction Unanno_Jn_Fraction 02H003 0 0 0.013449472 02H025 0 0 0.011203515 02H026 0 0 0.007282382 02H033 0 0 0.006310241 02H043 0 0 0.005871040 02H046 0 0 0.009819533 NMD_Jn_Fraction Fraction_Splice_Reads Fraction_Span_Reads IRBurden_clean 02H003 0.019509970 0.3506908 0.1735243 0.05796583 02H025 0.019360162 0.3712414 0.1591691 0.03963531 02H026 0.004298323 0.3980261 0.1615037 0.02576549 02H033 0.007705562 0.4003550 0.1734089 0.03090263 02H043 0.028069104 0.3671219 0.1807511 0.03762138 02H046 0.010542303 0.3725598 0.1603508 0.05099352 IRBurden_exitrons IRBurden_clean_unstranded IRBurden_exitrons_unstranded 02H003 0.1291810 0.03844293 0.1296020 02H025 0.1192351 0.02730399 0.1194005 02H026 0.1231055 0.02010410 0.1231939 02H033 0.1378958 0.02300500 0.1380215 02H043 0.1392935 0.02286515 0.1397365 02H046 0.1132136 0.03359077 0.1133852 IRBurden_antisense 02H003 0.021393335 02H025 0.013191532 02H026 0.006007119 02H033 0.008453742 02H043 0.015837096 02H046 0.019043703 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 45 ] > > # bump to trigger r cmd check > > proc.time() user system elapsed 416.263 235.973 660.561
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
name | user | system | elapsed | |
ASE-GLM-edgeR | 2.464 | 0.107 | 2.584 | |
ASE-methods | 35.012 | 0.282 | 35.661 | |
ASEFilter-class | 0.045 | 0.003 | 0.048 | |
Build-Reference-methods | 63.455 | 1.320 | 67.524 | |
Coverage | 0.960 | 0.038 | 1.002 | |
Gene-ontology-methods | 1.969 | 0.066 | 2.051 | |
Graphics-User-Interface | 0.000 | 0.001 | 0.001 | |
Mappability-methods | 3.022 | 0.038 | 3.084 | |
NxtSE-class | 65.611 | 1.014 | 67.104 | |
Run_SpliceWiz_Filters | 9.468 | 0.039 | 9.544 | |
STAR-methods | 0.006 | 0.012 | 0.030 | |
View-Reference-methods | 0.297 | 0.023 | 0.327 | |
collateData | 3.341 | 0.073 | 3.487 | |
coord2GR | 0.030 | 0.003 | 0.034 | |
covDataObject-class | 1.665 | 0.028 | 1.723 | |
covPlotObject-class | 21.757 | 0.449 | 22.386 | |
covPlotly-class | 1.067 | 0.019 | 1.089 | |
example-SpliceWiz-data | 0.017 | 0.003 | 0.020 | |
findSamples | 0.005 | 0.004 | 0.009 | |
isCOV | 0.018 | 0.004 | 0.022 | |
makeSE | 2.115 | 0.100 | 2.225 | |
make_plot_data | 0.051 | 0.003 | 0.055 | |
plotCoverage | 13.769 | 0.146 | 14.024 | |
processBAM | 4.937 | 0.653 | 4.025 | |
setSWthreads | 0.005 | 0.013 | 0.021 | |
theme_white | 0.167 | 0.057 | 0.229 | |