| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2023-12-05 11:37:14 -0500 (Tue, 05 Dec 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4688 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4421 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4440 |
| 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 1.4.0 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | 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: 1.4.0 |
| 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_1.4.0.tar.gz |
| StartedAt: 2023-12-05 06:21:03 -0500 (Tue, 05 Dec 2023) |
| EndedAt: 2023-12-05 06:33:43 -0500 (Tue, 05 Dec 2023) |
| EllapsedTime: 759.6 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_1.4.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/SpliceWiz.Rcheck'
* using R version 4.3.2 (2023-10-31 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 '1.4.0'
* 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 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 72.57 2.14 76.64
NxtSE-class 46.99 1.01 48.48
ASE-methods 29.44 0.22 29.77
covPlotObject-class 18.72 0.47 19.50
plotCoverage 11.39 0.15 11.55
Run_SpliceWiz_Filters 6.92 0.02 6.94
* 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 4.3.2 (2023-10-31 ucrt) -- "Eye Holes"
Copyright (C) 2023 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
Dec 05 6:30:40 AM Converting FASTA to local TwoBitFile...done
Dec 05 6:30:41 AM Connecting to genome TwoBitFile...done
Dec 05 6:30:41 AM Making local copy of GTF file...done
Dec 05 6:30:41 AM Extracting temp genome FASTA from TwoBit file
Dec 05 6:30:43 AM Generating synthetic reads, saving to F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Dec 05 6:30:43 AM Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.16.0
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 41.3GB / 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=71.6k bps/s ||
|| 16%, 0 mins elapsed, rate=139.3k bps/s ||
|| 24%, 0 mins elapsed, rate=203.6k bps/s ||
|| 33%, 0 mins elapsed, rate=264.6k bps/s ||
|| 41%, 0 mins elapsed, rate=322.9k bps/s ||
|| 49%, 0 mins elapsed, rate=379.8k bps/s ||
|| 58%, 0 mins elapsed, rate=434.1k bps/s ||
|| 66%, 0 mins elapsed, rate=486.0k bps/s ||
|| 74%, 0 mins elapsed, rate=532.0k bps/s ||
|| 83%, 0 mins elapsed, rate=580.8k bps/s ||
|| 91%, 0 mins elapsed, rate=627.6k 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=20.0k bps/s ||
|| 33%, 0 mins elapsed, rate=26.6k bps/s ||
|| 41%, 0 mins elapsed, rate=33.1k bps/s ||
|| 49%, 0 mins elapsed, rate=39.5k bps/s ||
|| 58%, 0 mins elapsed, rate=45.9k bps/s ||
|| 66%, 0 mins elapsed, rate=52.2k bps/s ||
|| 74%, 0 mins elapsed, rate=58.4k bps/s ||
|| 83%, 0 mins elapsed, rate=64.7k bps/s ||
|| 91%, 0 mins elapsed, rate=70.8k 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\RtmpmmZrth\refWithMapExcl\refe ... ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.16.0
//================================= 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 (05-Dec-2023 06:30:55, pid=25608) =================\\
|| ||
|| 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, 0.3 mins elapsed, rate=37.7k reads per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.4k reads per second ||
|| 99% completed, 0.4 mins elapsed, rate=0.5k 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 : 0.4 minutes ||
|| ||
\\============================================================================//
Dec 05 6:31:16 AM Calculating Mappability Exclusion regions from: F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Dec 05 6:31:20 AM Reference generated without non-polyA reference
Dec 05 6:31:20 AM Reference generated without Mappability reference
Dec 05 6:31:20 AM Reference generated without Blacklist exclusion
Dec 05 6:31:20 AM Converting FASTA to local TwoBitFile...done
Dec 05 6:31:21 AM Connecting to genome TwoBitFile...done
Dec 05 6:31:21 AM Making local copy of GTF file...done
Dec 05 6:31:22 AM Reading source GTF file...done
Dec 05 6:31:22 AM Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Dec 05 6:31:23 AM Gene ontology not prepared for this reference
Dec 05 6:31:25 AM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Dec 05 6:31:29 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
Dec 05 6:31:37 AM Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Dec 05 6:31:39 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
Dec 05 6:31:41 AM Splice Annotations Filtered
Dec 05 6:31:42 AM Translating Alternate Splice Peptides...done
Dec 05 6:31:42 AM Splice Annotations finished
Reference build finished
Dec 05 6:31:44 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\RtmpmmZrth\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\RtmpmmZrth\02H003.bam processed (487 milliseconds)
Dec 05 6:31:44 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\RtmpmmZrth\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\RtmpmmZrth\02H003.bam processed (310 milliseconds)
Dec 05 6:31:44 AM SpliceWiz reference already exists in given directory
Dec 05 6:31:44 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H003.bam processed (358 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H025.bam processed (311 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H026.bam processed (495 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H033.bam processed (428 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H043.bam processed (266 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H046.bam processed (514 milliseconds)
Dec 05 6:31:47 AM Validating Experiment; checking COV files...
Dec 05 6:31:47 AM Compiling Sample Stats
Dec 05 6:31:47 AM Compiling Junction List...merging...done
Dec 05 6:31:48 AM Compiling Junction Stats...merging...done
Dec 05 6:31:56 AM Compiling Intron Retention List...done
Dec 05 6:31:57 AM Compiling Tandem Junction List...merging...done
Dec 05 6:31:58 AM Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Dec 05 6:32:02 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
Dec 05 6:32:13 AM Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Dec 05 6:32:21 AM Generating NxtSE assays
Dec 05 6:32:39 AM Building Final NxtSE Object
Dec 05 6:32:39 AM ...consolidating assays to H5 file
Dec 05 6:32:41 AM ...packaging reference
Dec 05 6:32:41 AM ...synthesising NxtSE
Dec 05 6:32:42 AM ...determining how overlapping introns should be removed
Dec 05 6:32:45 AM SpliceWiz (NxtSE) Collation Finished
Dec 05 6:32:45 AM Loading NxtSE object from file...
Dec 05 6:32:45 AM ...loading reference (NxtSE)
Dec 05 6:32:45 AM ...linking assays
Dec 05 6:32:45 AM ...linking COV files
Dec 05 6:32:45 AM ...loading rowData
Dec 05 6:32:45 AM ...removing overlapping introns...
Dec 05 6:32:45 AM NxtSE loaded
Dec 05 6:32:45 AM SpliceWiz reference already exists in given directory
Dec 05 6:32:45 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H003.bam processed (347 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H025.bam processed (273 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H026.bam processed (427 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H033.bam processed (418 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H043.bam processed (279 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpmmZrth\02H046.bam processed (381 milliseconds)
Dec 05 6:32:47 AM Validating Experiment; checking COV files...
Dec 05 6:32:47 AM Compiling Sample Stats
Dec 05 6:32:47 AM Compiling Junction List...merging...done
Dec 05 6:32:49 AM Compiling Junction Stats...merging...done
Dec 05 6:32:56 AM Compiling Intron Retention List...done
Dec 05 6:32:58 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
Dec 05 6:33:08 AM Generating NxtSE assays
Dec 05 6:33:24 AM Building Final NxtSE Object
Dec 05 6:33:24 AM ...consolidating assays to H5 file
Dec 05 6:33:26 AM ...packaging reference
Dec 05 6:33:26 AM ...synthesising NxtSE
Dec 05 6:33:26 AM ...determining how overlapping introns should be removed
Dec 05 6:33:29 AM SpliceWiz (NxtSE) Collation Finished
Dec 05 6:33:29 AM Loading NxtSE object from file...
Dec 05 6:33:29 AM ...loading reference (NxtSE)
Dec 05 6:33:29 AM ...linking assays
Dec 05 6:33:29 AM ...linking COV files
Dec 05 6:33:29 AM ...loading rowData
Dec 05 6:33:29 AM ...removing overlapping introns...
Dec 05 6:33:29 AM NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 23 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
173.54 6.84 186.59
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 2.52 | 0.03 | 2.56 | |
| ASE-methods | 29.44 | 0.22 | 29.77 | |
| ASEFilter-class | 0.03 | 0.02 | 0.05 | |
| Build-Reference-methods | 72.57 | 2.14 | 76.64 | |
| Coverage | 0.81 | 0.04 | 0.86 | |
| Gene-ontology-methods | 1.45 | 0.08 | 1.62 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 2.42 | 0.02 | 3.15 | |
| NxtSE-class | 46.99 | 1.01 | 48.48 | |
| Run_SpliceWiz_Filters | 6.92 | 0.02 | 6.94 | |
| STAR-methods | 0 | 0 | 0 | |
| View-Reference-methods | 0.14 | 0.01 | 0.15 | |
| collateData | 0.30 | 0.04 | 0.33 | |
| coord2GR | 0.03 | 0.00 | 0.03 | |
| covDataObject-class | 1.28 | 0.03 | 1.35 | |
| covPlotObject-class | 18.72 | 0.47 | 19.50 | |
| covPlotly-class | 1.14 | 0.03 | 1.17 | |
| example-SpliceWiz-data | 0.01 | 0.00 | 0.01 | |
| findSamples | 0.04 | 0.00 | 0.04 | |
| isCOV | 0.01 | 0.00 | 0.01 | |
| makeSE | 0.53 | 0.09 | 0.63 | |
| make_plot_data | 0.05 | 0.02 | 0.06 | |
| plotCoverage | 11.39 | 0.15 | 11.55 | |
| processBAM | 2.56 | 0.08 | 1.54 | |
| setSWthreads | 0 | 0 | 0 | |
| theme_white | 0.12 | 0.00 | 0.12 | |