| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:37:21 -0400 (Wed, 17 Apr 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" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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: 2024-04-16 05:27:05 -0400 (Tue, 16 Apr 2024) |
| EndedAt: 2024-04-16 05:42:26 -0400 (Tue, 16 Apr 2024) |
| EllapsedTime: 920.8 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 81.57 2.20 86.17
NxtSE-class 54.75 0.89 56.03
ASE-methods 28.45 0.30 28.78
covPlotObject-class 22.40 0.47 22.88
plotCoverage 16.08 0.09 16.17
Run_SpliceWiz_Filters 8.13 0.05 8.17
* 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
Apr 16 5:38:01 AM Converting FASTA to local TwoBitFile...done
Apr 16 5:38:02 AM Connecting to genome TwoBitFile...done
Apr 16 5:38:02 AM Making local copy of GTF file...done
Apr 16 5:38:03 AM Extracting temp genome FASTA from TwoBit file
Apr 16 5:38:04 AM Generating synthetic reads, saving to F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Apr 16 5:38:04 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 : 40.3GB / 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=77.0k bps/s ||
|| 16%, 0 mins elapsed, rate=148.9k bps/s ||
|| 24%, 0 mins elapsed, rate=216.3k bps/s ||
|| 33%, 0 mins elapsed, rate=279.9k bps/s ||
|| 41%, 0 mins elapsed, rate=341.0k bps/s ||
|| 49%, 0 mins elapsed, rate=400.3k bps/s ||
|| 58%, 0 mins elapsed, rate=457.0k bps/s ||
|| 66%, 0 mins elapsed, rate=511.8k bps/s ||
|| 74%, 0 mins elapsed, rate=562.6k bps/s ||
|| 83%, 0 mins elapsed, rate=611.3k bps/s ||
|| 91%, 0 mins elapsed, rate=657.5k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=7.5k bps/s ||
|| 16%, 0 mins elapsed, rate=14.9k bps/s ||
|| 24%, 0 mins elapsed, rate=22.2k bps/s ||
|| 33%, 0 mins elapsed, rate=29.5k bps/s ||
|| 41%, 0 mins elapsed, rate=36.7k bps/s ||
|| 49%, 0 mins elapsed, rate=43.9k bps/s ||
|| 58%, 0 mins elapsed, rate=51.1k bps/s ||
|| 66%, 0 mins elapsed, rate=58.1k bps/s ||
|| 74%, 0 mins elapsed, rate=65.2k bps/s ||
|| 83%, 0 mins elapsed, rate=72.2k bps/s ||
|| 91%, 0 mins elapsed, rate=79.1k 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\RtmpKKswks\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 (16-Apr-2024 05:38:18, pid=74772) =================\\
|| ||
|| 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, 0.4 mins elapsed, rate=32.2k reads per second ||
|| 83% completed, 0.4 mins elapsed, rate=0.3k reads per second ||
|| 99% completed, 0.4 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 : 0.4 minutes ||
|| ||
\\============================================================================//
Apr 16 5:38:43 AM Calculating Mappability Exclusion regions from: F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\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%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Apr 16 5:38:48 AM Reference generated without non-polyA reference
Apr 16 5:38:48 AM Reference generated without Mappability reference
Apr 16 5:38:48 AM Reference generated without Blacklist exclusion
Apr 16 5:38:48 AM Converting FASTA to local TwoBitFile...done
Apr 16 5:38:49 AM Connecting to genome TwoBitFile...done
Apr 16 5:38:49 AM Making local copy of GTF file...done
Apr 16 5:38:55 AM Reading source GTF file...done
Apr 16 5:38:55 AM Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 16 5:38:56 AM Gene ontology not prepared for this reference
Apr 16 5:38:59 AM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 16 5:39:03 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
Apr 16 5:39:12 AM Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Apr 16 5:39:15 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
Apr 16 5:39:16 AM Splice Annotations Filtered
Apr 16 5:39:17 AM Translating Alternate Splice Peptides...done
Apr 16 5:39:18 AM Splice Annotations finished
Reference build finished
Apr 16 5:39:19 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\RtmpKKswks\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\RtmpKKswks\02H003.bam processed (395 milliseconds)
Apr 16 5:39:19 AM Running SpliceWiz processBAM
Reading reference file
Allocating memory to 2 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
Processing BAM file F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\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\RtmpKKswks\02H003.bam processed (306 milliseconds)
Apr 16 5:39:20 AM Reference generated without non-polyA reference
Apr 16 5:39:20 AM Reference generated without Mappability reference
Apr 16 5:39:20 AM Reference generated without Blacklist exclusion
Apr 16 5:39:20 AM Converting FASTA to local TwoBitFile...done
Apr 16 5:39:21 AM Connecting to genome TwoBitFile...done
Apr 16 5:39:21 AM Making local copy of GTF file...done
Apr 16 5:39:22 AM Reading source GTF file...done
Apr 16 5:39:22 AM Processing gtf file...
...genes
...transcripts
...CDS
Apr 16 5:39:23 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
Apr 16 5:39:23 AM Gene ontology not prepared for this reference
Apr 16 5:39:26 AM Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 16 5:39:30 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
Apr 16 5:39:37 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
Apr 16 5:39:39 AM Splice Annotations Filtered
Reference build finished
Apr 16 5:39:41 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H003.bam processed (354 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H025.bam processed (290 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H026.bam processed (533 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H033.bam processed (533 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H043.bam processed (379 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H046.bam processed (456 milliseconds)
Apr 16 5:39:44 AM Validating Experiment; checking COV files...
Apr 16 5:39:44 AM Compiling Sample Stats
Apr 16 5:39:44 AM Compiling Junction List...merging...done
Apr 16 5:39:45 AM Compiling Junction Stats...merging...done
Apr 16 5:39:53 AM Compiling Intron Retention List...done
Apr 16 5:39:55 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
Apr 16 5:40:06 AM Generating NxtSE assays
Apr 16 5:40:22 AM Building Final NxtSE Object
Apr 16 5:40:22 AM ...consolidating assays to H5 file
Apr 16 5:40:24 AM ...packaging reference
Apr 16 5:40:24 AM ...synthesising NxtSE
Apr 16 5:40:24 AM ...determining how overlapping introns should be removed
Apr 16 5:40:27 AM SpliceWiz (NxtSE) Collation Finished
Apr 16 5:40:27 AM Loading NxtSE object from file...
Apr 16 5:40:27 AM ...loading reference (NxtSE)
Apr 16 5:40:27 AM ...linking assays
Apr 16 5:40:27 AM ...linking COV files
Apr 16 5:40:27 AM ...loading rowData
Apr 16 5:40:28 AM ...removing overlapping introns...
Apr 16 5:40:28 AM NxtSE loaded
Apr 16 5:40:28 AM SpliceWiz reference already exists in given directory
Apr 16 5:40:28 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (1 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H003.bam processed (482 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H025.bam processed (306 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H026.bam processed (616 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H033.bam processed (534 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H043.bam processed (318 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H046.bam processed (542 milliseconds)
Apr 16 5:40:31 AM Validating Experiment; checking COV files...
Apr 16 5:40:31 AM Compiling Sample Stats
Apr 16 5:40:31 AM Compiling Junction List...merging...done
Apr 16 5:40:32 AM Compiling Junction Stats...merging...done
Apr 16 5:40:40 AM Compiling Intron Retention List...done
Apr 16 5:40:41 AM Compiling Tandem Junction List...merging...done
Apr 16 5:40:43 AM Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Apr 16 5:40:46 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
Apr 16 5:40:59 AM Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 16 5:41:07 AM Generating NxtSE assays
Apr 16 5:41:23 AM Building Final NxtSE Object
Apr 16 5:41:23 AM ...consolidating assays to H5 file
Apr 16 5:41:25 AM ...packaging reference
Apr 16 5:41:25 AM ...synthesising NxtSE
Apr 16 5:41:25 AM ...determining how overlapping introns should be removed
Apr 16 5:41:28 AM SpliceWiz (NxtSE) Collation Finished
Apr 16 5:41:28 AM Loading NxtSE object from file...
Apr 16 5:41:28 AM ...loading reference (NxtSE)
Apr 16 5:41:28 AM ...linking assays
Apr 16 5:41:28 AM ...linking COV files
Apr 16 5:41:28 AM ...loading rowData
Apr 16 5:41:28 AM ...removing overlapping introns...
Apr 16 5:41:28 AM NxtSE loaded
Apr 16 5:41:28 AM SpliceWiz reference already exists in given directory
Apr 16 5:41:28 AM Running SpliceWiz processBAM
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H003.bam processed (337 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H025.bam processed (278 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H026.bam processed (413 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H033.bam processed (441 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H043.bam processed (269 milliseconds)
F:\biocbuild\bbs-3.18-bioc\tmpdir\RtmpKKswks\02H046.bam processed (383 milliseconds)
Apr 16 5:41:31 AM Validating Experiment; checking COV files...
Apr 16 5:41:31 AM Compiling Sample Stats
Apr 16 5:41:31 AM Compiling Junction List...merging...done
Apr 16 5:41:32 AM Compiling Junction Stats...merging...done
Apr 16 5:41:39 AM Compiling Intron Retention List...done
Apr 16 5:41:40 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
Apr 16 5:41:51 AM Generating NxtSE assays
Apr 16 5:42:07 AM Building Final NxtSE Object
Apr 16 5:42:07 AM ...consolidating assays to H5 file
Apr 16 5:42:08 AM ...packaging reference
Apr 16 5:42:09 AM ...synthesising NxtSE
Apr 16 5:42:09 AM ...determining how overlapping introns should be removed
Apr 16 5:42:11 AM SpliceWiz (NxtSE) Collation Finished
Apr 16 5:42:11 AM Loading NxtSE object from file...
Apr 16 5:42:11 AM ...loading reference (NxtSE)
Apr 16 5:42:11 AM ...linking assays
Apr 16 5:42:11 AM ...linking COV files
Apr 16 5:42:11 AM ...loading rowData
Apr 16 5:42:11 AM ...removing overlapping introns...
Apr 16 5:42:12 AM NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
251.95 8.10 269.78
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 4.04 | 0.09 | 4.12 | |
| ASE-methods | 28.45 | 0.30 | 28.78 | |
| ASEFilter-class | 0.07 | 0.00 | 0.06 | |
| Build-Reference-methods | 81.57 | 2.20 | 86.17 | |
| Coverage | 0.93 | 0.02 | 0.94 | |
| Gene-ontology-methods | 1.98 | 0.03 | 2.02 | |
| Graphics-User-Interface | 0.02 | 0.00 | 0.01 | |
| Mappability-methods | 2.67 | 0.03 | 3.43 | |
| NxtSE-class | 54.75 | 0.89 | 56.03 | |
| Run_SpliceWiz_Filters | 8.13 | 0.05 | 8.17 | |
| STAR-methods | 0 | 0 | 0 | |
| View-Reference-methods | 0.22 | 0.03 | 0.25 | |
| collateData | 0.39 | 0.11 | 0.50 | |
| coord2GR | 0.01 | 0.02 | 0.03 | |
| covDataObject-class | 1.82 | 0.00 | 2.00 | |
| covPlotObject-class | 22.40 | 0.47 | 22.88 | |
| covPlotly-class | 0.91 | 0.09 | 1.00 | |
| example-SpliceWiz-data | 0.01 | 0.00 | 0.01 | |
| findSamples | 0.00 | 0.02 | 0.02 | |
| isCOV | 0.02 | 0.00 | 0.01 | |
| makeSE | 0.69 | 0.09 | 0.78 | |
| make_plot_data | 0.03 | 0.02 | 0.05 | |
| plotCoverage | 16.08 | 0.09 | 16.17 | |
| processBAM | 2.51 | 0.09 | 1.67 | |
| setSWthreads | 0 | 0 | 0 | |
| theme_white | 0.19 | 0.03 | 0.22 | |