| Back to Multiple platform build/check report for BioC 3.16: simplified long |
|
This page was generated on 2023-04-12 11:06:28 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4502 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" | 4282 |
| lconway | macOS 12.5.1 Monterey | x86_64 | 4.2.3 (2023-03-15) -- "Shortstop Beagle" | 4310 |
| 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 | ||||
|
To the developers/maintainers of the SpliceWiz package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1945/2183 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SpliceWiz 1.0.4 (landing page) Alex Chit Hei Wong
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.5.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: SpliceWiz |
| Version: 1.0.4 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.0.4.tar.gz |
| StartedAt: 2023-04-10 22:52:12 -0400 (Mon, 10 Apr 2023) |
| EndedAt: 2023-04-10 23:06:03 -0400 (Mon, 10 Apr 2023) |
| EllapsedTime: 831.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SpliceWiz.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.0.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.16-bioc/meat/SpliceWiz.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.0.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpliceWiz’ can be installed ... OK
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
NxtSE-class 42.415 0.770 43.322
ASE-methods 34.938 0.355 35.408
Build-Reference-methods 14.847 0.173 15.052
plotCoverage 7.786 0.159 7.972
Run_SpliceWiz_Filters 6.188 0.022 6.224
* 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: 1 NOTE
See
‘/Users/biocbuild/bbs-3.16-bioc/meat/SpliceWiz.Rcheck/00check.log’
for details.
SpliceWiz.Rcheck/00install.out
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL SpliceWiz
###
##############################################################################
##############################################################################
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘SpliceWiz’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c FastaReader.cpp -o FastaReader.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c GZTools.cpp -o GZTools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
ReadBlockProcessor_CoverageBlocks.cpp:251:16: warning: variable 'len' set but not used [-Wunused-but-set-variable]
unsigned int len=0;
^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c covTools.cpp -o covTools.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c main.cpp -o main.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c swEngine.cpp -o swEngine.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RcppProgress/include' -I/usr/local/include -DSPLICEWIZ -fPIC -Wall -g -O2 -c synthReadGenerator.cpp -o synthReadGenerator.o
clang++ -mmacosx-version-min=10.13 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o SpliceWiz.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -DSPLICEWIZ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.2/Resources/library/00LOCK-SpliceWiz/00new/SpliceWiz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpliceWiz)
SpliceWiz.Rcheck/tests/testthat.Rout
R version 4.2.3 (2023-03-15) -- "Shortstop Beagle"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 1 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Apr 10 22:58:53 Converting FASTA to local TwoBitFile...done
Apr 10 22:58:54 Connecting to genome TwoBitFile...done
Apr 10 22:58:54 Making local copy of GTF file...done
Apr 10 22:58:55 Extracting temp genome FASTA from TwoBit file
Apr 10 22:58:55 Generating synthetic reads, saving to /private/tmp/RtmpbJtWCy/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Apr 10 22:58:55 Cleaning temp genome / gene annotation files
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= setting ==================================\\
|| ||
|| Index name : reference_index ||
|| Index space : base space ||
|| Index split : no-split ||
|| Repeat threshold : 100 repeats ||
|| Gapped index : no ||
|| ||
|| Free / total memory : 58.8GB / 96.0GB ||
|| ||
|| 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=44.0k bps/s ||
|| 16%, 0 mins elapsed, rate=86.6k bps/s ||
|| 24%, 0 mins elapsed, rate=128.0k bps/s ||
|| 33%, 0 mins elapsed, rate=168.4k bps/s ||
|| 41%, 0 mins elapsed, rate=207.9k bps/s ||
|| 49%, 0 mins elapsed, rate=246.7k bps/s ||
|| 58%, 0 mins elapsed, rate=284.1k bps/s ||
|| 66%, 0 mins elapsed, rate=320.4k bps/s ||
|| 74%, 0 mins elapsed, rate=356.1k bps/s ||
|| 83%, 0 mins elapsed, rate=390.9k bps/s ||
|| 91%, 0 mins elapsed, rate=424.2k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=5.3k bps/s ||
|| 16%, 0 mins elapsed, rate=10.5k bps/s ||
|| 24%, 0 mins elapsed, rate=15.7k bps/s ||
|| 33%, 0 mins elapsed, rate=20.9k bps/s ||
|| 41%, 0 mins elapsed, rate=26.1k bps/s ||
|| 49%, 0 mins elapsed, rate=31.2k bps/s ||
|| 58%, 0 mins elapsed, rate=36.4k bps/s ||
|| 66%, 0 mins elapsed, rate=41.5k bps/s ||
|| 74%, 0 mins elapsed, rate=46.6k bps/s ||
|| 83%, 0 mins elapsed, rate=51.7k bps/s ||
|| 91%, 0 mins elapsed, rate=56.7k 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: 0.3 minutes. ||
|| Index ./reference_index was successfully built. ||
|| ||
\\============================================================================//
========== _____ _ _ ____ _____ ______ _____
===== / ____| | | | _ \| __ \| ____| /\ | __ \
===== | (___ | | | | |_) | |__) | |__ / \ | | | |
==== \___ \| | | | _ <| _ /| __| / /\ \ | | | |
==== ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
========== |_____/ \____/|____/|_| \_\______/_/ \_\_____/
Rsubread 2.12.3
//================================= 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 (10-Apr-2023 22:59:12, pid=9730) =================\\
|| ||
|| 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, 4.9 mins elapsed, rate=42.7k reads per second ||
|| 83% completed, 4.9 mins elapsed, rate=0.0k reads per second ||
|| 99% completed, 4.9 mins elapsed, rate=0.0k reads per second ||
|| ||
|| Completed successfully. ||
|| ||
\\==================================== ====================================//
//================================ Summary =================================\\
|| ||
|| Total reads : 10,145 ||
|| Mapped : 10,145 (100.0%) ||
|| Uniquely mapped : 10,145 ||
|| Multi-mapping : 0 ||
|| ||
|| Unmapped : 0 ||
|| ||
|| Junctions : 0 ||
|| Indels : 1 ||
|| ||
|| Running time : 4.9 minutes ||
|| ||
\\============================================================================//
Apr 10 23:04:03 Calculating Mappability Exclusion regions from: /tmp/RtmpbJtWCy/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmpbJtWCy/refWithMapExcl/Mappability/AlignedReads.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing Mappability Exclusions
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
SpliceWiz was compiled without OpenMP
Apr 10 23:04:06 Reference generated without non-polyA reference
Apr 10 23:04:06 Reference generated without Mappability reference
Apr 10 23:04:06 Reference generated without Blacklist exclusion
Apr 10 23:04:06 Converting FASTA to local TwoBitFile...done
Apr 10 23:04:07 Connecting to genome TwoBitFile...done
Apr 10 23:04:07 Making local copy of GTF file...done
Apr 10 23:04:07 Reading source GTF file...done
Apr 10 23:04:08 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 10 23:04:10 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 10 23:04:13 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 10 23:04:20 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Apr 10 23:04:21 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 10 23:04:22 Splice Annotations Filtered
Apr 10 23:04:22 Translating Alternate Splice Peptides...done
Apr 10 23:04:22 Splice Annotations finished
Reference build finished
Apr 10 23:04:22 Running SpliceWiz processBAM
Apr 10 23:04:22 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmpbJtWCy/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
**************************************************|
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Writing output file
/private/tmp/RtmpbJtWCy/02H003.bam processed (354 milliseconds)
Apr 10 23:04:23 SpliceWiz processBAM processed RtmpbJtWCy/02H003.bam
Apr 10 23:04:23 Running SpliceWiz processBAM
Apr 10 23:04:23 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmpbJtWCy/02H003.bam
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
Performing final sort of fragment maps
Writing COV file
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Writing output file
/private/tmp/RtmpbJtWCy/02H003.bam processed (381 milliseconds)
Apr 10 23:04:23 SpliceWiz processBAM processed RtmpbJtWCy/02H003.bam
Apr 10 23:04:23 SpliceWiz reference already exists in given directory
Apr 10 23:04:23 Running SpliceWiz processBAM
Apr 10 23:04:23 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpbJtWCy/02H003.bam processed (352 milliseconds)
Apr 10 23:04:24 SpliceWiz processBAM processed RtmpbJtWCy/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpbJtWCy/02H025.bam processed (261 milliseconds)
Apr 10 23:04:24 SpliceWiz processBAM processed RtmpbJtWCy/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpbJtWCy/02H026.bam processed (403 milliseconds)
Apr 10 23:04:24 SpliceWiz processBAM processed RtmpbJtWCy/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpbJtWCy/02H033.bam processed (461 milliseconds)
Apr 10 23:04:25 SpliceWiz processBAM processed RtmpbJtWCy/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpbJtWCy/02H043.bam processed (301 milliseconds)
Apr 10 23:04:25 SpliceWiz processBAM processed RtmpbJtWCy/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpbJtWCy/02H046.bam processed (401 milliseconds)
Apr 10 23:04:25 SpliceWiz processBAM processed RtmpbJtWCy/02H046.bam
Apr 10 23:04:26 Using MulticoreParam 1 threads
Apr 10 23:04:26 Validating Experiment; checking COV files...
Apr 10 23:04:26 Compiling Sample Stats
Apr 10 23:04:26 Compiling Junction List...merging...done
Apr 10 23:04:27 Compiling Junction Stats...merging...done
Apr 10 23:04:33 Compiling Intron Retention List...done
Apr 10 23:04:34 Compiling Tandem Junction List...merging...done
Apr 10 23:04:35 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Apr 10 23:04:38 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 10 23:04:47 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 10 23:04:53 Generating NxtSE assays
Apr 10 23:04:53 Using MulticoreParam 1 threads
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Apr 10 23:05:07 Building Final NxtSE Object
Apr 10 23:05:09 SpliceWiz (NxtSE) Collation Finished
Apr 10 23:05:09 Loading NxtSE object from file...done
Apr 10 23:05:10 Removing overlapping introns...
Apr 10 23:05:10 Iterating through IR events to determine introns of main isoforms
Apr 10 23:05:11 Iteration 1
Apr 10 23:05:12 Iteration 2
Apr 10 23:05:14 SpliceWiz reference already exists in given directory
Apr 10 23:05:14 processBAM has already been run on given BAM files
Apr 10 23:05:14 Using MulticoreParam 1 threads
Apr 10 23:05:14 Validating Experiment; checking COV files...
Apr 10 23:05:14 Compiling Sample Stats
Apr 10 23:05:14 Compiling Junction List...merging...done
Apr 10 23:05:15 Compiling Junction Stats...merging...done
Apr 10 23:05:22 Compiling Intron Retention List...done
Apr 10 23:05:23 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 10 23:05:31 Generating NxtSE assays
Apr 10 23:05:31 Using MulticoreParam 1 threads
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Apr 10 23:05:44 Building Final NxtSE Object
Apr 10 23:05:46 SpliceWiz (NxtSE) Collation Finished
Apr 10 23:05:46 Loading NxtSE object from file...done
Apr 10 23:05:47 Removing overlapping introns...
Apr 10 23:05:47 Iterating through IR events to determine introns of main isoforms
Apr 10 23:05:48 Iteration 1
Apr 10 23:05:49 Iteration 2
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 29 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
265.054 161.776 431.319
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-methods | 34.938 | 0.355 | 35.408 | |
| ASEFilter-class | 0.040 | 0.003 | 0.043 | |
| Build-Reference-methods | 14.847 | 0.173 | 15.052 | |
| Coverage | 0.763 | 0.030 | 0.800 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 1.119 | 0.026 | 1.149 | |
| NxtSE-class | 42.415 | 0.770 | 43.322 | |
| Run_SpliceWiz_Filters | 6.188 | 0.022 | 6.224 | |
| STAR-methods | 0.003 | 0.005 | 0.020 | |
| View-Reference-methods | 0.007 | 0.005 | 0.013 | |
| collateData | 0.066 | 0.020 | 0.112 | |
| coord2GR | 0.013 | 0.002 | 0.015 | |
| example-SpliceWiz-data | 0.005 | 0.001 | 0.007 | |
| findSamples | 0.004 | 0.002 | 0.006 | |
| isCOV | 0.006 | 0.002 | 0.010 | |
| makeSE | 4.438 | 0.088 | 4.566 | |
| make_plot_data | 3.832 | 0.011 | 3.851 | |
| plotCoverage | 7.786 | 0.159 | 7.972 | |
| processBAM | 2.311 | 1.107 | 2.200 | |
| setSWthreads | 0.475 | 0.240 | 0.027 | |
| theme_white | 0.159 | 0.082 | 0.243 | |