Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:06 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 2039/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpliceWiz 1.8.0 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
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: 1.8.0 |
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_1.8.0.tar.gz |
StartedAt: 2024-12-20 10:09:35 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 10:43:19 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 2023.8 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_1.8.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/SpliceWiz.Rcheck’ * using R version 4.4.2 (2024-10-31) * using platform: x86_64-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 Monterey 12.7.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpliceWiz/DESCRIPTION’ ... OK * this is package ‘SpliceWiz’ version ‘1.8.0’ * 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 14.0.0 (clang-1400.0.29.202)’ * 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 Build-Reference-methods 77.998 2.847 84.346 NxtSE-class 67.315 1.684 70.608 ASE-methods 48.550 0.600 50.759 covPlotObject-class 43.262 0.633 44.934 plotCoverage 31.508 0.217 32.295 Run_SpliceWiz_Filters 8.853 0.040 9.134 processBAM 5.936 1.231 4.747 ASE-GLM-edgeR 5.072 0.283 5.454 * 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-3.20-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-x86_64/Resources/library’ * installing *source* package ‘SpliceWiz’ ... ** using staged installation Configuring without OpenMP for MacOS ** libs using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’ using C++11 using SDK: ‘MacOSX11.3.sdk’ clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c BAM2blocks.cpp -o BAM2blocks.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FastaReader.cpp -o FastaReader.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FragmentBlocks.cpp -o FragmentBlocks.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c GZTools.cpp -o GZTools.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/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 x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c covTools.cpp -o covTools.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c swEngine.cpp -o swEngine.o clang++ -arch x86_64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/RcppProgress/include' -I/opt/R/x86_64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c synthReadGenerator.cpp -o synthReadGenerator.o clang++ -arch x86_64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/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-x86_64/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 4.4.2 (2024-10-31) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-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 2 threads Use setSWthreads() to set the number of SpliceWiz threads > > test_check("SpliceWiz") Loading required package: Rsubread Dec 20 10:26:50 Converting FASTA to local TwoBitFile...done Dec 20 10:26:51 Connecting to genome TwoBitFile...done Dec 20 10:26:51 Making local copy of GTF file...done Dec 20 10:26:51 Extracting temp genome FASTA from TwoBit file Dec 20 10:26:52 Generating synthetic reads, saving to /private/tmp/Rtmpy9xjfW/refWithMapExcl/Mappability/Reads.fa 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 10145 synthetic reads generated Dec 20 10:26:52 Cleaning temp genome / gene annotation files ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.20.0 //================================= setting ==================================\\ || || || Index name : reference_index || || Index space : base space || || Index split : no-split || || Repeat threshold : 100 repeats || || Gapped index : no || || || || Free / total memory : 36.1GB / 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=27.2k bps/s || || 16%, 0 mins elapsed, rate=53.7k bps/s || || 24%, 0 mins elapsed, rate=79.7k bps/s || || 33%, 0 mins elapsed, rate=105.0k bps/s || || 41%, 0 mins elapsed, rate=129.8k bps/s || || 49%, 0 mins elapsed, rate=154.1k bps/s || || 58%, 0 mins elapsed, rate=177.9k bps/s || || 66%, 0 mins elapsed, rate=201.0k bps/s || || 74%, 0 mins elapsed, rate=223.7k bps/s || || 83%, 0 mins elapsed, rate=246.3k bps/s || || 91%, 0 mins elapsed, rate=268.4k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=2.9k bps/s || || 16%, 0 mins elapsed, rate=5.8k bps/s || || 24%, 0 mins elapsed, rate=8.6k bps/s || || 33%, 0 mins elapsed, rate=11.5k bps/s || || 41%, 0 mins elapsed, rate=14.3k bps/s || || 49%, 0 mins elapsed, rate=17.1k bps/s || || 58%, 0 mins elapsed, rate=20.0k bps/s || || 66%, 0 mins elapsed, rate=22.8k bps/s || || 74%, 0 mins elapsed, rate=25.6k bps/s || || 83%, 0 mins elapsed, rate=28.4k bps/s || || 91%, 0 mins elapsed, rate=31.2k 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: 0.6 minutes. || || Index ./reference_index was successfully built. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.20.0 //================================= 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 (20-Dec-2024 10:27:30, pid=5458) =================\\ || || || 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, 10 mins elapsed, rate=18.7k reads per second || || 83% completed, 10 mins elapsed, rate=0.0k reads per second || || 99% completed, 10 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 : 10.5 minutes || || || \\============================================================================// Dec 20 10:38:02 Calculating Mappability Exclusion regions from: /tmp/Rtmpy9xjfW/refWithMapExcl/Mappability/AlignedReads.bam Calculating Mappability Exclusions: /private/tmp/Rtmpy9xjfW/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 Dec 20 10:38:09 Reference generated without non-polyA reference Dec 20 10:38:09 Reference generated without Mappability reference Dec 20 10:38:09 Reference generated without Blacklist exclusion Dec 20 10:38:09 Converting FASTA to local TwoBitFile...done Dec 20 10:38:11 Connecting to genome TwoBitFile...done Dec 20 10:38:11 Making local copy of GTF file...done Dec 20 10:38:11 Reading source GTF file...done Dec 20 10:38:11 Processing gtf file... ...genes ...transcripts ...CDS ...exons done Dec 20 10:38:14 Gene ontology not prepared for this reference Dec 20 10:38:16 Processing introns... ...data ...basic annotations ...splice motifs ...other info ...defining flanking exon clusters done Dec 20 10:38:22 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 Dec 20 10:38:33 Predicting NMD transcripts from genome sequence ...exonic transcripts ...retained introns | | | 0% | |======================================================================| 100% done Dec 20 10:38:36 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 Dec 20 10:38:38 Splice Annotations Filtered Dec 20 10:38:39 Translating Alternate Splice Peptides...done Dec 20 10:38:40 Splice Annotations finished Reference build finished Dec 20 10:38:41 Running SpliceWiz processBAM Dec 20 10:38:42 Using MulticoreParam 1 threads Reading reference file Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) Processing BAM file /private/tmp/Rtmpy9xjfW/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/Rtmpy9xjfW/02H003.bam processed (724 milliseconds) Dec 20 10:38:43 SpliceWiz processBAM processed Rtmpy9xjfW/02H003.bam Dec 20 10:38:43 Running SpliceWiz processBAM Dec 20 10:38:44 Using MulticoreParam 1 threads Reading reference file Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) Processing BAM file /private/tmp/Rtmpy9xjfW/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/Rtmpy9xjfW/02H003.bam processed (716 milliseconds) Dec 20 10:38:45 SpliceWiz processBAM processed Rtmpy9xjfW/02H003.bam Dec 20 10:38:45 Reference generated without non-polyA reference Dec 20 10:38:45 Reference generated without Mappability reference Dec 20 10:38:45 Reference generated without Blacklist exclusion Dec 20 10:38:45 Converting FASTA to local TwoBitFile...done Dec 20 10:38:46 Connecting to genome TwoBitFile...done Dec 20 10:38:47 Making local copy of GTF file...done Dec 20 10:38:47 Reading source GTF file...done Dec 20 10:38:47 Processing gtf file... ...genes ...transcripts ...CDS Dec 20 10:38:48 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 Dec 20 10:38:49 Gene ontology not prepared for this reference Dec 20 10:38:52 Processing introns... ...data ...basic annotations ...splice motifs ...other info ...defining flanking exon clusters done Dec 20 10:38:57 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 Dec 20 10:39:07 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 Dec 20 10:39:08 Splice Annotations Filtered Reference build finished Dec 20 10:39:11 Running SpliceWiz processBAM Dec 20 10:39:12 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H003.bam processed (723 milliseconds) Dec 20 10:39:13 SpliceWiz processBAM processed Rtmpy9xjfW/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H025.bam processed (563 milliseconds) Dec 20 10:39:13 SpliceWiz processBAM processed Rtmpy9xjfW/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H026.bam processed (882 milliseconds) Dec 20 10:39:14 SpliceWiz processBAM processed Rtmpy9xjfW/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H033.bam processed (865 milliseconds) Dec 20 10:39:15 SpliceWiz processBAM processed Rtmpy9xjfW/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H043.bam processed (550 milliseconds) Dec 20 10:39:16 SpliceWiz processBAM processed Rtmpy9xjfW/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H046.bam processed (799 milliseconds) Dec 20 10:39:17 SpliceWiz processBAM processed Rtmpy9xjfW/02H046.bam Dec 20 10:39:18 Using MulticoreParam 1 threads Dec 20 10:39:18 Validating Experiment; checking COV files... Dec 20 10:39:18 Compiling Sample Stats Dec 20 10:39:18 Compiling Junction List...merging...done Dec 20 10:39:19 Compiling Junction Stats...merging...done Dec 20 10:39:27 Compiling Intron Retention List...done Dec 20 10:39:28 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...copying splicing reference ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Dec 20 10:39:41 Generating NxtSE assays Dec 20 10:39:42 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Dec 20 10:40:01 Building Final NxtSE Object Dec 20 10:40:01 ...consolidating assays to H5 file Dec 20 10:40:03 ...packaging reference Dec 20 10:40:03 ...synthesising NxtSE Dec 20 10:40:04 ...determining how overlapping introns should be removed Dec 20 10:40:08 SpliceWiz (NxtSE) Collation Finished Dec 20 10:40:08 Loading NxtSE object from file... Dec 20 10:40:08 ...loading reference (NxtSE) Dec 20 10:40:08 ...linking assays Dec 20 10:40:08 ...linking COV files Dec 20 10:40:08 ...loading rowData Dec 20 10:40:08 ...removing overlapping introns... Dec 20 10:40:08 NxtSE loaded Dec 20 10:40:09 SpliceWiz reference already exists in given directory Dec 20 10:40:09 Running SpliceWiz processBAM Dec 20 10:40:10 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H003.bam processed (703 milliseconds) Dec 20 10:40:11 SpliceWiz processBAM processed Rtmpy9xjfW/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H025.bam processed (578 milliseconds) Dec 20 10:40:12 SpliceWiz processBAM processed Rtmpy9xjfW/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H026.bam processed (860 milliseconds) Dec 20 10:40:12 SpliceWiz processBAM processed Rtmpy9xjfW/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H033.bam processed (935 milliseconds) Dec 20 10:40:13 SpliceWiz processBAM processed Rtmpy9xjfW/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H043.bam processed (546 milliseconds) Dec 20 10:40:14 SpliceWiz processBAM processed Rtmpy9xjfW/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H046.bam processed (777 milliseconds) Dec 20 10:40:15 SpliceWiz processBAM processed Rtmpy9xjfW/02H046.bam Dec 20 10:40:16 Using MulticoreParam 1 threads Dec 20 10:40:16 Validating Experiment; checking COV files... Dec 20 10:40:16 Compiling Sample Stats Dec 20 10:40:16 Compiling Junction List...merging...done Dec 20 10:40:17 Compiling Junction Stats...merging...done Dec 20 10:40:25 Compiling Intron Retention List...done Dec 20 10:40:27 Compiling Tandem Junction List...merging...done Dec 20 10:40:28 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...looking for novel exons Dec 20 10:40:32 Assembling novel splicing reference: ...loading reference FASTA/GTF ...injecting novel transcripts to GTF ...processing GTF ...processing introns from GTF ...annotating alternative splicing events done Dec 20 10:40:47 Tidying up splice junctions and intron retentions (part 2)... ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Dec 20 10:40:57 Generating NxtSE assays Dec 20 10:40:58 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Dec 20 10:41:17 Building Final NxtSE Object Dec 20 10:41:17 ...consolidating assays to H5 file Dec 20 10:41:19 ...packaging reference Dec 20 10:41:19 ...synthesising NxtSE Dec 20 10:41:19 ...determining how overlapping introns should be removed Dec 20 10:41:23 SpliceWiz (NxtSE) Collation Finished Dec 20 10:41:23 Loading NxtSE object from file... Dec 20 10:41:23 ...loading reference (NxtSE) Dec 20 10:41:23 ...linking assays Dec 20 10:41:23 ...linking COV files Dec 20 10:41:23 ...loading rowData Dec 20 10:41:24 ...removing overlapping introns... Dec 20 10:41:24 NxtSE loaded Dec 20 10:41:25 SpliceWiz reference already exists in given directory Dec 20 10:41:25 Running SpliceWiz processBAM Dec 20 10:41:26 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H003.bam processed (718 milliseconds) Dec 20 10:41:27 SpliceWiz processBAM processed Rtmpy9xjfW/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H025.bam processed (583 milliseconds) Dec 20 10:41:27 SpliceWiz processBAM processed Rtmpy9xjfW/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H026.bam processed (864 milliseconds) Dec 20 10:41:28 SpliceWiz processBAM processed Rtmpy9xjfW/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H033.bam processed (867 milliseconds) Dec 20 10:41:29 SpliceWiz processBAM processed Rtmpy9xjfW/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H043.bam processed (539 milliseconds) Dec 20 10:41:30 SpliceWiz processBAM processed Rtmpy9xjfW/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/Rtmpy9xjfW/02H046.bam processed (793 milliseconds) Dec 20 10:41:30 SpliceWiz processBAM processed Rtmpy9xjfW/02H046.bam Dec 20 10:41:32 Using MulticoreParam 1 threads Dec 20 10:41:32 Validating Experiment; checking COV files... Dec 20 10:41:32 Compiling Sample Stats Dec 20 10:41:32 Compiling Junction List...merging...done Dec 20 10:41:33 Compiling Junction Stats...merging...done Dec 20 10:41:41 Compiling Intron Retention List...done Dec 20 10:41:42 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...copying splicing reference ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Dec 20 10:41:55 Generating NxtSE assays Dec 20 10:41:56 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Dec 20 10:42:15 Building Final NxtSE Object Dec 20 10:42:15 ...consolidating assays to H5 file Dec 20 10:42:17 ...packaging reference Dec 20 10:42:17 ...synthesising NxtSE Dec 20 10:42:17 ...determining how overlapping introns should be removed Dec 20 10:42:21 SpliceWiz (NxtSE) Collation Finished Dec 20 10:42:21 Loading NxtSE object from file... Dec 20 10:42:21 ...loading reference (NxtSE) Dec 20 10:42:21 ...linking assays Dec 20 10:42:21 ...linking COV files Dec 20 10:42:21 ...loading rowData Dec 20 10:42:21 ...removing overlapping introns... Dec 20 10:42:22 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 MD5 is fcdc53e0f7fbd843529077ebd26dd058 Dec 20 10:42:26 Reference generated without non-polyA reference Dec 20 10:42:26 Reference generated without Mappability reference Dec 20 10:42:26 Reference generated without Blacklist exclusion Dec 20 10:42:26 Converting FASTA to local TwoBitFile...done Dec 20 10:42:27 Connecting to genome TwoBitFile...done Dec 20 10:42:27 Making local copy of GTF file...done Dec 20 10:42:27 Reading source GTF file...done Dec 20 10:42:28 Processing gtf file... ...genes ...transcripts ...CDS ...exons done Dec 20 10:42:30 Gene ontology not prepared for this reference Dec 20 10:42:32 Processing introns... ...data ...basic annotations ...splice motifs ...other info ...defining flanking exon clusters done Dec 20 10:42:37 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 Dec 20 10:42:48 Predicting NMD transcripts from genome sequence ...exonic transcripts ...retained introns | | | 0% | |======================================================================| 100% done Dec 20 10:42:51 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 Dec 20 10:42:53 Splice Annotations Filtered Dec 20 10:42:54 Translating Alternate Splice Peptides...done Dec 20 10:42:54 Splice Annotations finished Reference build finished [ FAIL 0 | WARN 0 | SKIP 0 | PASS 47 ] > > # bump to trigger r cmd check > > proc.time() user system elapsed 572.174 350.920 997.759
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
name | user | system | elapsed | |
ASE-GLM-edgeR | 5.072 | 0.283 | 5.454 | |
ASE-methods | 48.550 | 0.600 | 50.759 | |
ASEFilter-class | 0.116 | 0.008 | 0.131 | |
Build-Reference-methods | 77.998 | 2.847 | 84.346 | |
Coverage | 2.018 | 0.046 | 2.221 | |
Gene-ontology-methods | 4.227 | 0.088 | 4.555 | |
Graphics-User-Interface | 0.001 | 0.001 | 0.001 | |
Mappability-methods | 2.616 | 0.054 | 2.836 | |
NxtSE-class | 67.315 | 1.684 | 70.608 | |
Run_SpliceWiz_Filters | 8.853 | 0.040 | 9.134 | |
STAR-methods | 0.007 | 0.013 | 0.028 | |
View-Reference-methods | 0.338 | 0.035 | 0.379 | |
collateData | 3.209 | 0.086 | 3.341 | |
coord2GR | 0.048 | 0.003 | 0.052 | |
covDataObject-class | 3.650 | 0.047 | 3.747 | |
covPlotObject-class | 43.262 | 0.633 | 44.934 | |
covPlotly-class | 2.423 | 0.023 | 2.487 | |
example-SpliceWiz-data | 0.024 | 0.004 | 0.028 | |
findSamples | 0.010 | 0.006 | 0.017 | |
isCOV | 0.022 | 0.005 | 0.026 | |
makeSE | 2.749 | 0.175 | 2.952 | |
make_plot_data | 0.107 | 0.004 | 0.133 | |
plotCoverage | 31.508 | 0.217 | 32.295 | |
processBAM | 5.936 | 1.231 | 4.747 | |
setSWthreads | 0.004 | 0.017 | 0.027 | |
theme_white | 0.306 | 0.092 | 0.400 | |