Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-03-29 11:38:17 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 2030/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
SpliceWiz 1.4.1 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
To the developers/maintainers of the SpliceWiz package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SpliceWiz.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: SpliceWiz |
Version: 1.4.1 |
Command: /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_1.4.1.tar.gz |
StartedAt: 2024-03-28 09:23:23 -0400 (Thu, 28 Mar 2024) |
EndedAt: 2024-03-28 09:58:31 -0400 (Thu, 28 Mar 2024) |
EllapsedTime: 2108.1 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_1.4.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * 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 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘SpliceWiz/DESCRIPTION’ ... OK * this is package ‘SpliceWiz’ version ‘1.4.1’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘SpliceWiz’ can be installed ... OK * used C++ compiler: ‘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 ... 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 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 127.613 3.964 149.965 NxtSE-class 66.733 1.610 72.650 ASE-methods 48.252 0.784 52.203 covPlotObject-class 44.126 0.701 53.852 plotCoverage 30.263 0.261 32.759 Run_SpliceWiz_Filters 9.052 0.059 10.001 processBAM 6.011 1.436 5.396 ASE-GLM-edgeR 5.222 0.194 5.917 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/Users/biocbuild/bbs-3.18-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/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-x86_64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-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/4.3-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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin20 (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 1 threads Use setSWthreads() to set the number of SpliceWiz threads > > test_check("SpliceWiz") Loading required package: Rsubread Mar 28 09:42:28 Converting FASTA to local TwoBitFile...done Mar 28 09:42:29 Connecting to genome TwoBitFile...done Mar 28 09:42:29 Making local copy of GTF file...done Mar 28 09:42:30 Extracting temp genome FASTA from TwoBit file Mar 28 09:42:31 Generating synthetic reads, saving to /private/tmp/RtmpcF1GTY/refWithMapExcl/Mappability/Reads.fa 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| 10145 synthetic reads generated Mar 28 09:42:31 Cleaning temp genome / gene annotation files ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.16.1 //================================= setting ==================================\\ || || || Index name : reference_index || || Index space : base space || || Index split : no-split || || Repeat threshold : 100 repeats || || Gapped index : no || || || || Free / total memory : 30.9GB / 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=22.1k bps/s || || 16%, 0 mins elapsed, rate=43.7k bps/s || || 24%, 0 mins elapsed, rate=64.8k bps/s || || 33%, 0 mins elapsed, rate=85.6k bps/s || || 41%, 0 mins elapsed, rate=106.0k bps/s || || 49%, 0 mins elapsed, rate=126.1k bps/s || || 58%, 0 mins elapsed, rate=145.3k bps/s || || 66%, 0 mins elapsed, rate=164.7k bps/s || || 74%, 0 mins elapsed, rate=183.8k bps/s || || 83%, 0 mins elapsed, rate=202.0k bps/s || || 91%, 0 mins elapsed, rate=220.6k bps/s || || 3.0 GB of memory is needed for index building. || || Build the index... || || 8%, 0 mins elapsed, rate=2.5k bps/s || || 16%, 0 mins elapsed, rate=4.9k bps/s || || 24%, 0 mins elapsed, rate=7.4k bps/s || || 33%, 0 mins elapsed, rate=9.8k bps/s || || 41%, 0 mins elapsed, rate=12.3k bps/s || || 49%, 0 mins elapsed, rate=14.7k bps/s || || 58%, 0 mins elapsed, rate=17.1k bps/s || || 66%, 0 mins elapsed, rate=19.5k bps/s || || 74%, 0 mins elapsed, rate=21.9k bps/s || || 83%, 0 mins elapsed, rate=24.3k bps/s || || 91%, 0 mins elapsed, rate=26.7k 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: 0.7 minutes. || || Index ./reference_index was successfully built. || || || \\============================================================================// ========== _____ _ _ ____ _____ ______ _____ ===== / ____| | | | _ \| __ \| ____| /\ | __ \ ===== | (___ | | | | |_) | |__) | |__ / \ | | | | ==== \___ \| | | | _ <| _ /| __| / /\ \ | | | | ==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| | ========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/ Rsubread 2.16.1 //================================= setting ==================================\\ || || || Function : Read alignment + Junction detection (RNA-Seq) || || Input file : Reads.fa || || Output file : AlignedReads.bam (BAM) || || Index name : reference_index || || || || ------------------------------------ || || || || Threads : 1 || || Phred offset : 33 || || Min votes : 1 / 14 || || Max mismatches : 3 || || Max indel length : 5 || || Report multi-mapping reads : yes || || Max alignments per multi-mapping read : 1 || || Annotations : transcripts.gtf (GTF) || || || \\============================================================================// //================ Running (28-Mar-2024 09:43:13, pid=31225) =================\\ || || || 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=18.9k 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 || || || \\============================================================================// Mar 28 09:53:41 Calculating Mappability Exclusion regions from: /tmp/RtmpcF1GTY/refWithMapExcl/Mappability/AlignedReads.bam Calculating Mappability Exclusions: /private/tmp/RtmpcF1GTY/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 Mar 28 09:53:49 Reference generated without non-polyA reference Mar 28 09:53:49 Reference generated without Mappability reference Mar 28 09:53:49 Reference generated without Blacklist exclusion Mar 28 09:53:49 Converting FASTA to local TwoBitFile...done Mar 28 09:53:50 Connecting to genome TwoBitFile...done Mar 28 09:53:50 Making local copy of GTF file...done Mar 28 09:53:50 Reading source GTF file...done Mar 28 09:53:51 Processing gtf file... ...genes ...transcripts ...CDS ...exons done Mar 28 09:53:54 Gene ontology not prepared for this reference Mar 28 09:53:56 Processing introns... ...data ...basic annotations ...splice motifs ...other info ...defining flanking exon clusters done Mar 28 09:54:01 Generating processBAM reference ...prepping data ...determining measurable introns (directional) ...determining measurable introns (non-directional) ...writing ref-cover.bed ...writing ref-ROI.bed ...writing ref-read-continues.ref ...writing ref-sj.ref ...writing ref-tj.ref processBAM reference generated Mar 28 09:54:13 Predicting NMD transcripts from genome sequence ...exonic transcripts ...retained introns | | | 0% | |======================================================================| 100% done Mar 28 09:54:16 Annotating Splice Events Annotating Mutually-Exclusive-Exon Splice Events...done Annotating Skipped-Exon Splice Events...done Annotating Alternate 5' / 3' Splice Site Splice Events...done Annotating Alternate First / Last Exon Splice Events...done Annotating known retained introns...done Mar 28 09:54:17 Splice Annotations Filtered Mar 28 09:54:19 Translating Alternate Splice Peptides...done Mar 28 09:54:19 Splice Annotations finished Reference build finished Mar 28 09:54:20 Running SpliceWiz processBAM Mar 28 09:54:22 Using MulticoreParam 1 threads Reading reference file Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (4 milliseconds) Processing BAM file /private/tmp/RtmpcF1GTY/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/RtmpcF1GTY/02H003.bam processed (838 milliseconds) Mar 28 09:54:23 SpliceWiz processBAM processed RtmpcF1GTY/02H003.bam Mar 28 09:54:23 Running SpliceWiz processBAM Mar 28 09:54:24 Using MulticoreParam 1 threads Reading reference file Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) Processing BAM file /private/tmp/RtmpcF1GTY/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/RtmpcF1GTY/02H003.bam processed (805 milliseconds) Mar 28 09:54:25 SpliceWiz processBAM processed RtmpcF1GTY/02H003.bam Mar 28 09:54:25 Reference generated without non-polyA reference Mar 28 09:54:25 Reference generated without Mappability reference Mar 28 09:54:25 Reference generated without Blacklist exclusion Mar 28 09:54:25 Converting FASTA to local TwoBitFile...done Mar 28 09:54:27 Connecting to genome TwoBitFile...done Mar 28 09:54:27 Making local copy of GTF file...done Mar 28 09:54:27 Reading source GTF file...done Mar 28 09:54:27 Processing gtf file... ...genes ...transcripts ...CDS Mar 28 09:54:28 No protein information detected in reference! For full functionality, ensure there are valid entries with type == `CDS` in the gtf file. Protein reference and NMD annotation is skipped. ...exons done Mar 28 09:54:29 Gene ontology not prepared for this reference Mar 28 09:54:32 Processing introns... ...data ...basic annotations ...splice motifs ...other info ...defining flanking exon clusters done Mar 28 09:54:37 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 Mar 28 09:54:47 Annotating Splice Events Annotating Mutually-Exclusive-Exon Splice Events...done Annotating Skipped-Exon Splice Events...done Annotating Alternate 5' / 3' Splice Site Splice Events...done Annotating Alternate First / Last Exon Splice Events...done Annotating known retained introns...done Mar 28 09:54:49 Splice Annotations Filtered Reference build finished Mar 28 09:54:51 Running SpliceWiz processBAM Mar 28 09:54:53 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H003.bam processed (769 milliseconds) Mar 28 09:54:53 SpliceWiz processBAM processed RtmpcF1GTY/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H025.bam processed (597 milliseconds) Mar 28 09:54:54 SpliceWiz processBAM processed RtmpcF1GTY/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H026.bam processed (943 milliseconds) Mar 28 09:54:55 SpliceWiz processBAM processed RtmpcF1GTY/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H033.bam processed (928 milliseconds) Mar 28 09:54:56 SpliceWiz processBAM processed RtmpcF1GTY/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H043.bam processed (591 milliseconds) Mar 28 09:54:57 SpliceWiz processBAM processed RtmpcF1GTY/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H046.bam processed (852 milliseconds) Mar 28 09:54:57 SpliceWiz processBAM processed RtmpcF1GTY/02H046.bam Mar 28 09:54:59 Using MulticoreParam 1 threads Mar 28 09:54:59 Validating Experiment; checking COV files... Mar 28 09:54:59 Compiling Sample Stats Mar 28 09:54:59 Compiling Junction List...merging...done Mar 28 09:55:00 Compiling Junction Stats...merging...done Mar 28 09:55:09 Compiling Intron Retention List...done Mar 28 09:55:10 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...copying splicing reference ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Mar 28 09:55:23 Generating NxtSE assays Mar 28 09:55:24 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Mar 28 09:55:43 Building Final NxtSE Object Mar 28 09:55:43 ...consolidating assays to H5 file Mar 28 09:55:46 ...packaging reference Mar 28 09:55:46 ...synthesising NxtSE Mar 28 09:55:47 ...determining how overlapping introns should be removed Mar 28 09:55:50 SpliceWiz (NxtSE) Collation Finished Mar 28 09:55:50 Loading NxtSE object from file... Mar 28 09:55:50 ...loading reference (NxtSE) Mar 28 09:55:50 ...linking assays Mar 28 09:55:50 ...linking COV files Mar 28 09:55:50 ...loading rowData Mar 28 09:55:51 ...removing overlapping introns... Mar 28 09:55:51 NxtSE loaded Mar 28 09:55:52 SpliceWiz reference already exists in given directory Mar 28 09:55:52 Running SpliceWiz processBAM Mar 28 09:55:53 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H003.bam processed (778 milliseconds) Mar 28 09:55:54 SpliceWiz processBAM processed RtmpcF1GTY/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H025.bam processed (644 milliseconds) Mar 28 09:55:55 SpliceWiz processBAM processed RtmpcF1GTY/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H026.bam processed (949 milliseconds) Mar 28 09:55:56 SpliceWiz processBAM processed RtmpcF1GTY/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H033.bam processed (948 milliseconds) Mar 28 09:55:57 SpliceWiz processBAM processed RtmpcF1GTY/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H043.bam processed (612 milliseconds) Mar 28 09:55:57 SpliceWiz processBAM processed RtmpcF1GTY/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H046.bam processed (892 milliseconds) Mar 28 09:55:58 SpliceWiz processBAM processed RtmpcF1GTY/02H046.bam Mar 28 09:55:59 Using MulticoreParam 1 threads Mar 28 09:55:59 Validating Experiment; checking COV files... Mar 28 09:55:59 Compiling Sample Stats Mar 28 09:56:00 Compiling Junction List...merging...done Mar 28 09:56:01 Compiling Junction Stats...merging...done Mar 28 09:56:09 Compiling Intron Retention List...done Mar 28 09:56:11 Compiling Tandem Junction List...merging...done Mar 28 09:56:12 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...looking for novel exons Mar 28 09:56:16 Assembling novel splicing reference: ...loading reference FASTA/GTF ...injecting novel transcripts to GTF ...processing GTF ...processing introns from GTF ...annotating alternative splicing events done Mar 28 09:56:32 Tidying up splice junctions and intron retentions (part 2)... ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Mar 28 09:56:43 Generating NxtSE assays Mar 28 09:56:44 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Mar 28 09:57:04 Building Final NxtSE Object Mar 28 09:57:04 ...consolidating assays to H5 file Mar 28 09:57:06 ...packaging reference Mar 28 09:57:06 ...synthesising NxtSE Mar 28 09:57:07 ...determining how overlapping introns should be removed Mar 28 09:57:10 SpliceWiz (NxtSE) Collation Finished Mar 28 09:57:10 Loading NxtSE object from file... Mar 28 09:57:10 ...loading reference (NxtSE) Mar 28 09:57:10 ...linking assays Mar 28 09:57:10 ...linking COV files Mar 28 09:57:10 ...loading rowData Mar 28 09:57:10 ...removing overlapping introns... Mar 28 09:57:11 NxtSE loaded Mar 28 09:57:11 SpliceWiz reference already exists in given directory Mar 28 09:57:11 Running SpliceWiz processBAM Mar 28 09:57:13 Using MulticoreParam 1 threads Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H003.bam processed (800 milliseconds) Mar 28 09:57:14 SpliceWiz processBAM processed RtmpcF1GTY/02H003.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H025.bam processed (614 milliseconds) Mar 28 09:57:14 SpliceWiz processBAM processed RtmpcF1GTY/02H025.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H026.bam processed (923 milliseconds) Mar 28 09:57:15 SpliceWiz processBAM processed RtmpcF1GTY/02H026.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H033.bam processed (918 milliseconds) Mar 28 09:57:16 SpliceWiz processBAM processed RtmpcF1GTY/02H033.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H043.bam processed (568 milliseconds) Mar 28 09:57:17 SpliceWiz processBAM processed RtmpcF1GTY/02H043.bam Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds) /private/tmp/RtmpcF1GTY/02H046.bam processed (832 milliseconds) Mar 28 09:57:18 SpliceWiz processBAM processed RtmpcF1GTY/02H046.bam Mar 28 09:57:19 Using MulticoreParam 1 threads Mar 28 09:57:19 Validating Experiment; checking COV files... Mar 28 09:57:19 Compiling Sample Stats Mar 28 09:57:19 Compiling Junction List...merging...done Mar 28 09:57:20 Compiling Junction Stats...merging...done Mar 28 09:57:30 Compiling Intron Retention List...done Mar 28 09:57:31 Tidying up splice junctions and intron retentions... ...annotating splice junctions ...copying splicing reference ...grouping splice junctions ...grouping introns ...loading splice events ...compiling rowEvents done Mar 28 09:57:45 Generating NxtSE assays Mar 28 09:57:46 Using MulticoreParam 1 threads | | | 0% | |============ | 17% | |======================= | 33% | |=================================== | 50% | |=============================================== | 67% | |========================================================== | 83% | |======================================================================| 100% Mar 28 09:58:05 Building Final NxtSE Object Mar 28 09:58:05 ...consolidating assays to H5 file Mar 28 09:58:07 ...packaging reference Mar 28 09:58:08 ...synthesising NxtSE Mar 28 09:58:08 ...determining how overlapping introns should be removed Mar 28 09:58:11 SpliceWiz (NxtSE) Collation Finished Mar 28 09:58:11 Loading NxtSE object from file... Mar 28 09:58:11 ...loading reference (NxtSE) Mar 28 09:58:11 ...linking assays Mar 28 09:58:11 ...linking COV files Mar 28 09:58:11 ...loading rowData Mar 28 09:58:12 ...removing overlapping introns... Mar 28 09:58:12 NxtSE loaded [ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ] > > # bump to trigger r cmd check > > proc.time() user system elapsed 536.912 345.773 980.049
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
name | user | system | elapsed | |
ASE-GLM-edgeR | 5.222 | 0.194 | 5.917 | |
ASE-methods | 48.252 | 0.784 | 52.203 | |
ASEFilter-class | 0.116 | 0.011 | 0.148 | |
Build-Reference-methods | 127.613 | 3.964 | 149.965 | |
Coverage | 1.929 | 0.065 | 2.176 | |
Gene-ontology-methods | 3.755 | 0.128 | 4.039 | |
Graphics-User-Interface | 0.001 | 0.001 | 0.001 | |
Mappability-methods | 2.684 | 0.071 | 2.869 | |
NxtSE-class | 66.733 | 1.610 | 72.650 | |
Run_SpliceWiz_Filters | 9.052 | 0.059 | 10.001 | |
STAR-methods | 0.007 | 0.018 | 0.058 | |
View-Reference-methods | 0.303 | 0.032 | 0.355 | |
collateData | 3.223 | 0.086 | 3.482 | |
coord2GR | 0.048 | 0.003 | 0.051 | |
covDataObject-class | 3.530 | 0.050 | 3.888 | |
covPlotObject-class | 44.126 | 0.701 | 53.852 | |
covPlotly-class | 2.277 | 0.029 | 2.493 | |
example-SpliceWiz-data | 0.025 | 0.004 | 0.034 | |
findSamples | 0.011 | 0.007 | 0.020 | |
isCOV | 0.025 | 0.006 | 0.032 | |
makeSE | 2.495 | 0.141 | 2.780 | |
make_plot_data | 0.106 | 0.004 | 0.117 | |
plotCoverage | 30.263 | 0.261 | 32.759 | |
processBAM | 6.011 | 1.436 | 5.396 | |
setSWthreads | 0.005 | 0.019 | 0.025 | |
theme_white | 0.295 | 0.095 | 0.404 | |