| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:37:21 -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: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpliceWiz.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SpliceWiz_1.4.1.tar.gz |
| StartedAt: 2024-03-28 05:30:16 -0400 (Thu, 28 Mar 2024) |
| EndedAt: 2024-03-28 05:45:47 -0400 (Thu, 28 Mar 2024) |
| EllapsedTime: 930.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:SpliceWiz.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings SpliceWiz_1.4.1.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 whether package 'SpliceWiz' can be installed ... OK
* used C++ compiler: 'G__~1.EXE (GCC) 12.3.0'
* 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 for x64 is not available
File 'F:/biocbuild/bbs-3.18-bioc/R/library/SpliceWiz/libs/x64/SpliceWiz.dll':
Found '_assert', possibly from 'assert' (C)
Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Build-Reference-methods 80.11 2.10 85.11
NxtSE-class 52.22 0.95 53.61
ASE-methods 31.75 0.28 32.05
covPlotObject-class 25.12 0.54 25.67
plotCoverage 16.00 0.16 16.15
Run_SpliceWiz_Filters 7.51 0.00 7.51
* 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
'F:/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck/00check.log'
for details.
SpliceWiz.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL SpliceWiz ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'SpliceWiz' ... ** using staged installation ** libs using C++ compiler: 'G__~1.EXE (GCC) 12.3.0' using C++11 g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c BAM2blocks.cpp -o BAM2blocks.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FastaReader.cpp -o FastaReader.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c FragmentBlocks.cpp -o FragmentBlocks.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c GZTools.cpp -o GZTools.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c covTools.cpp -o covTools.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c main.cpp -o main.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c swEngine.cpp -o swEngine.o g++ -std=gnu++11 -I"F:/biocbuild/bbs-3.18-bioc/R/include" -DNDEBUG -I'F:/biocbuild/bbs-3.18-bioc/R/library/ompBAM/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/include' -I'F:/biocbuild/bbs-3.18-bioc/R/library/RcppProgress/include' -I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -fopenmp -DSPLICEWIZ -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c synthReadGenerator.cpp -o synthReadGenerator.o g++ -shared -s -static-libgcc -o SpliceWiz.dll tmp.def BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -fopenmp -DSPLICEWIZ -LF:/biocbuild/bbs-3.18-bioc/R/library/zlibbioc/libs/x64 -lzlib1bioc -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools43/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.18-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.18-bioc/R/library/00LOCK-SpliceWiz/00new/SpliceWiz/libs/x64 ** 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 ** 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 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 2 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Mar 28 5:41:15 AM Converting FASTA to local TwoBitFile...done
Mar 28 5:41:17 AM Connecting to genome TwoBitFile...done
Mar 28 5:41:17 AM Making local copy of GTF file...done
Mar 28 5:41:17 AM Extracting temp genome FASTA from TwoBit file
Mar 28 5:41:19 AM Generating synthetic reads, saving to F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Mar 28 5:41:19 AM 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 : 37.2GB / 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=67.5k bps/s ||
|| 16%, 0 mins elapsed, rate=130.8k bps/s ||
|| 24%, 0 mins elapsed, rate=190.6k bps/s ||
|| 33%, 0 mins elapsed, rate=247.2k bps/s ||
|| 41%, 0 mins elapsed, rate=301.1k bps/s ||
|| 49%, 0 mins elapsed, rate=352.6k bps/s ||
|| 58%, 0 mins elapsed, rate=401.1k bps/s ||
|| 66%, 0 mins elapsed, rate=447.8k bps/s ||
|| 74%, 0 mins elapsed, rate=492.8k bps/s ||
|| 83%, 0 mins elapsed, rate=536.1k bps/s ||
|| 91%, 0 mins elapsed, rate=577.4k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=6.7k bps/s ||
|| 16%, 0 mins elapsed, rate=13.4k bps/s ||
|| 24%, 0 mins elapsed, rate=19.9k bps/s ||
|| 33%, 0 mins elapsed, rate=26.5k bps/s ||
|| 41%, 0 mins elapsed, rate=33.0k bps/s ||
|| 49%, 0 mins elapsed, rate=39.4k bps/s ||
|| 58%, 0 mins elapsed, rate=45.8k bps/s ||
|| 66%, 0 mins elapsed, rate=52.1k bps/s ||
|| 74%, 0 mins elapsed, rate=58.3k bps/s ||
|| 83%, 0 mins elapsed, rate=64.6k bps/s ||
|| 91%, 0 mins elapsed, rate=70.7k 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: 0.2 minutes. ||
||Index F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\refWithMapExcl\refe ... ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
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 05:41:32, pid=76772) =================\\
|| ||
|| Check the input reads. ||
|| The input file contains base space reads. ||
|| Initialise the memory objects. ||
|| Estimate the mean read length. ||
|| Create the output BAM file. ||
|| Check the index. ||
|| Init the voting space. ||
|| Load the annotation file. ||
|| 538 annotation records were loaded. ||
|| Global environment is initialised. ||
|| Load the 1-th index block... ||
|| The index block has been loaded. ||
|| Start read mapping in chunk. ||
|| 65% completed, 0.5 mins elapsed, rate=27.6k reads per second ||
|| 83% completed, 0.5 mins elapsed, rate=0.3k reads per second ||
|| 99% completed, 0.5 mins elapsed, rate=0.4k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 10145 ||
|| Mapped : 10145 (100.0%) ||
|| Uniquely mapped : 10145 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 0 ||
|| ||
|| Junctions : 0 ||
|| Indels : 1 ||
|| ||
|| Running time : 0.5 minutes ||
|| ||
\\============================================================================//
Mar 28 5:42:00 AM Calculating Mappability Exclusion regions from: F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\refWithMapExcl\Mappability\AlignedReads.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing Mappability Exclusions
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Mar 28 5:42:05 AM Reference generated without non-polyA reference
Mar 28 5:42:05 AM Reference generated without Mappability reference
Mar 28 5:42:05 AM Reference generated without Blacklist exclusion
Mar 28 5:42:05 AM Converting FASTA to local TwoBitFile...done
Mar 28 5:42:06 AM Connecting to genome TwoBitFile...done
Mar 28 5:42:06 AM Making local copy of GTF file...done
Mar 28 5:42:07 AM Reading source GTF file...done
Mar 28 5:42:07 AM Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Mar 28 5:42:09 AM Gene ontology not prepared for this reference
Mar 28 5:42:11 AM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 28 5:42:16 AM 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 5:42:23 AM Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Mar 28 5:42:26 AM 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 5:42:27 AM Splice Annotations Filtered
Mar 28 5:42:28 AM Translating Alternate Splice Peptides...done
Mar 28 5:42:29 AM Splice Annotations finished
Reference build finished
Mar 28 5:42:30 AM Running SpliceWiz processBAM
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\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
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H003.bam processed (414 milliseconds)
Mar 28 5:42:30 AM Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (2 milliseconds)
Processing BAM file F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Compiling data from threads
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H003.bam processed (308 milliseconds)
Mar 28 5:42:31 AM Reference generated without non-polyA reference
Mar 28 5:42:31 AM Reference generated without Mappability reference
Mar 28 5:42:31 AM Reference generated without Blacklist exclusion
Mar 28 5:42:31 AM Converting FASTA to local TwoBitFile...done
Mar 28 5:42:32 AM Connecting to genome TwoBitFile...done
Mar 28 5:42:32 AM Making local copy of GTF file...done
Mar 28 5:42:33 AM Reading source GTF file...done
Mar 28 5:42:33 AM Processing gtf file...
...genes
...transcripts
...CDS
Mar 28 5:42:33 AM 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 5:42:34 AM Gene ontology not prepared for this reference
Mar 28 5:42:37 AM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Mar 28 5:42:41 AM 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 5:42:49 AM 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 5:42:50 AM Splice Annotations Filtered
Reference build finished
Mar 28 5:42:53 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H003.bam processed (462 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H025.bam processed (389 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H026.bam processed (548 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H033.bam processed (452 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H043.bam processed (368 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H046.bam processed (435 milliseconds)
Mar 28 5:42:55 AM Validating Experiment; checking COV files...
Mar 28 5:42:55 AM Compiling Sample Stats
Mar 28 5:42:55 AM Compiling Junction List...merging...done
Mar 28 5:42:57 AM Compiling Junction Stats...merging...done
Mar 28 5:43:05 AM Compiling Intron Retention List...done
Mar 28 5:43:06 AM 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 5:43:18 AM Generating NxtSE assays
Mar 28 5:43:34 AM Building Final NxtSE Object
Mar 28 5:43:34 AM ...consolidating assays to H5 file
Mar 28 5:43:36 AM ...packaging reference
Mar 28 5:43:36 AM ...synthesising NxtSE
Mar 28 5:43:36 AM ...determining how overlapping introns should be removed
Mar 28 5:43:40 AM SpliceWiz (NxtSE) Collation Finished
Mar 28 5:43:40 AM Loading NxtSE object from file...
Mar 28 5:43:40 AM ...loading reference (NxtSE)
Mar 28 5:43:40 AM ...linking assays
Mar 28 5:43:40 AM ...linking COV files
Mar 28 5:43:40 AM ...loading rowData
Mar 28 5:43:40 AM ...removing overlapping introns...
Mar 28 5:43:40 AM NxtSE loaded
Mar 28 5:43:41 AM SpliceWiz reference already exists in given directory
Mar 28 5:43:41 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H003.bam processed (456 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H025.bam processed (409 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H026.bam processed (560 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H033.bam processed (577 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H043.bam processed (384 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H046.bam processed (505 milliseconds)
Mar 28 5:43:44 AM Validating Experiment; checking COV files...
Mar 28 5:43:44 AM Compiling Sample Stats
Mar 28 5:43:44 AM Compiling Junction List...merging...done
Mar 28 5:43:45 AM Compiling Junction Stats...merging...done
Mar 28 5:43:53 AM Compiling Intron Retention List...done
Mar 28 5:43:55 AM Compiling Tandem Junction List...merging...done
Mar 28 5:43:56 AM Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Mar 28 5:44:00 AM 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 5:44:13 AM Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Mar 28 5:44:22 AM Generating NxtSE assays
Mar 28 5:44:38 AM Building Final NxtSE Object
Mar 28 5:44:38 AM ...consolidating assays to H5 file
Mar 28 5:44:40 AM ...packaging reference
Mar 28 5:44:40 AM ...synthesising NxtSE
Mar 28 5:44:40 AM ...determining how overlapping introns should be removed
Mar 28 5:44:43 AM SpliceWiz (NxtSE) Collation Finished
Mar 28 5:44:43 AM Loading NxtSE object from file...
Mar 28 5:44:43 AM ...loading reference (NxtSE)
Mar 28 5:44:43 AM ...linking assays
Mar 28 5:44:43 AM ...linking COV files
Mar 28 5:44:43 AM ...loading rowData
Mar 28 5:44:44 AM ...removing overlapping introns...
Mar 28 5:44:44 AM NxtSE loaded
Mar 28 5:44:44 AM SpliceWiz reference already exists in given directory
Mar 28 5:44:44 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H003.bam processed (484 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H025.bam processed (374 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H026.bam processed (451 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H033.bam processed (432 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H043.bam processed (273 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpqYmDNa\02H046.bam processed (470 milliseconds)
Mar 28 5:44:47 AM Validating Experiment; checking COV files...
Mar 28 5:44:47 AM Compiling Sample Stats
Mar 28 5:44:47 AM Compiling Junction List...merging...done
Mar 28 5:44:48 AM Compiling Junction Stats...merging...done
Mar 28 5:44:56 AM Compiling Intron Retention List...done
Mar 28 5:44:57 AM 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 5:45:09 AM Generating NxtSE assays
Mar 28 5:45:25 AM Building Final NxtSE Object
Mar 28 5:45:25 AM ...consolidating assays to H5 file
Mar 28 5:45:27 AM ...packaging reference
Mar 28 5:45:27 AM ...synthesising NxtSE
Mar 28 5:45:28 AM ...determining how overlapping introns should be removed
Mar 28 5:45:31 AM SpliceWiz (NxtSE) Collation Finished
Mar 28 5:45:31 AM Loading NxtSE object from file...
Mar 28 5:45:31 AM ...loading reference (NxtSE)
Mar 28 5:45:31 AM ...linking assays
Mar 28 5:45:31 AM ...linking COV files
Mar 28 5:45:31 AM ...loading rowData
Mar 28 5:45:31 AM ...removing overlapping introns...
Mar 28 5:45:31 AM NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
260.50 8.84 274.78
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 4.14 | 0.14 | 4.28 | |
| ASE-methods | 31.75 | 0.28 | 32.05 | |
| ASEFilter-class | 0.06 | 0.00 | 0.06 | |
| Build-Reference-methods | 80.11 | 2.10 | 85.11 | |
| Coverage | 0.90 | 0.04 | 0.94 | |
| Gene-ontology-methods | 1.94 | 0.14 | 2.07 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 2.83 | 0.08 | 3.74 | |
| NxtSE-class | 52.22 | 0.95 | 53.61 | |
| Run_SpliceWiz_Filters | 7.51 | 0.00 | 7.51 | |
| STAR-methods | 0 | 0 | 0 | |
| View-Reference-methods | 0.16 | 0.00 | 0.16 | |
| collateData | 0.29 | 0.04 | 0.32 | |
| coord2GR | 0.03 | 0.00 | 0.03 | |
| covDataObject-class | 1.71 | 0.00 | 1.71 | |
| covPlotObject-class | 25.12 | 0.54 | 25.67 | |
| covPlotly-class | 1.22 | 0.06 | 1.28 | |
| example-SpliceWiz-data | 0.01 | 0.00 | 0.01 | |
| findSamples | 0.02 | 0.02 | 0.03 | |
| isCOV | 0.00 | 0.02 | 0.02 | |
| makeSE | 0.76 | 0.09 | 0.86 | |
| make_plot_data | 0.05 | 0.00 | 0.05 | |
| plotCoverage | 16.00 | 0.16 | 16.15 | |
| processBAM | 2.48 | 0.06 | 1.60 | |
| setSWthreads | 0 | 0 | 0 | |
| theme_white | 0.24 | 0.00 | 0.23 | |