| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-04-18 11:32:19 -0400 (Thu, 18 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4388 |
| 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
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the SpliceWiz package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: SpliceWiz |
| Version: 1.4.1 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:SpliceWiz.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings SpliceWiz_1.4.1.tar.gz |
| StartedAt: 2024-04-18 05:04:00 -0400 (Thu, 18 Apr 2024) |
| EndedAt: 2024-04-18 05:26:49 -0400 (Thu, 18 Apr 2024) |
| EllapsedTime: 1369.1 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_1.4.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/SpliceWiz.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SpliceWiz/DESCRIPTION’ ... OK
* this is package ‘SpliceWiz’ version ‘1.4.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SpliceWiz’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
* used SDK: ‘MacOSX11.3.sdk’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in shell scripts ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
Build-Reference-methods 84.851 1.587 90.582
NxtSE-class 65.834 0.917 69.109
ASE-methods 36.919 0.295 37.735
covPlotObject-class 20.683 0.475 21.580
plotCoverage 13.722 0.178 14.046
Run_SpliceWiz_Filters 9.316 0.044 9.565
processBAM 5.072 0.721 3.992
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/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/4.3-arm64/Resources/library’
* installing *source* package ‘SpliceWiz’ ...
** using staged installation
Configuring without OpenMP for MacOS
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’
using C++11
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c BAM2blocks.cpp -o BAM2blocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FastaReader.cpp -o FastaReader.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c FragmentBlocks.cpp -o FragmentBlocks.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c GZTools.cpp -o GZTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor.cpp -o ReadBlockProcessor.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_CoverageBlocks.cpp -o ReadBlockProcessor_CoverageBlocks.o
ReadBlockProcessor_CoverageBlocks.cpp:251:16: warning: variable 'len' set but not used [-Wunused-but-set-variable]
unsigned int len=0;
^
1 warning generated.
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_FragmentsMap.cpp -o ReadBlockProcessor_FragmentsMap.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c ReadBlockProcessor_TandemJunctions.cpp -o ReadBlockProcessor_TandemJunctions.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c covTools.cpp -o covTools.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c main.cpp -o main.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c swEngine.cpp -o swEngine.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/ompBAM/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/zlibbioc/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppProgress/include' -I/opt/R/arm64/include -DSPLICEWIZ -fPIC -falign-functions=64 -Wall -g -O2 -c synthReadGenerator.cpp -o synthReadGenerator.o
clang++ -arch arm64 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o SpliceWiz.so BAM2blocks.o FastaReader.o FragmentBlocks.o GZTools.o RcppExports.o ReadBlockProcessor.o ReadBlockProcessor_CoverageBlocks.o ReadBlockProcessor_FragmentsMap.o ReadBlockProcessor_TandemJunctions.o covTools.o main.o swEngine.o synthReadGenerator.o -DSPLICEWIZ -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/00LOCK-SpliceWiz/00new/SpliceWiz/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SpliceWiz)
SpliceWiz.Rcheck/tests/testthat.Rout
R version 4.3.3 (2024-02-29) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(SpliceWiz)
Loading required package: NxtIRFdata
SpliceWiz package loaded with 1 threads
Use setSWthreads() to set the number of SpliceWiz threads
>
> test_check("SpliceWiz")
Loading required package: Rsubread
Apr 18 05:15:44 Converting FASTA to local TwoBitFile...done
Apr 18 05:15:46 Connecting to genome TwoBitFile...done
Apr 18 05:15:46 Making local copy of GTF file...done
Apr 18 05:15:46 Extracting temp genome FASTA from TwoBit file
Apr 18 05:15:47 Generating synthetic reads, saving to /private/tmp/RtmpNH2q4b/refWithMapExcl/Mappability/Reads.fa
0% 10 20 30 40 50 60 70 80 90 100%
[----|----|----|----|----|----|----|----|----|----|
**************************************************|
10145 synthetic reads generated
Apr 18 05:15:47 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 : 33.6GB / 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=87.2k bps/s ||
|| 16%, 0 mins elapsed, rate=164.3k bps/s ||
|| 24%, 0 mins elapsed, rate=234.1k bps/s ||
|| 33%, 0 mins elapsed, rate=299.0k bps/s ||
|| 41%, 0 mins elapsed, rate=362.4k bps/s ||
|| 49%, 0 mins elapsed, rate=423.8k bps/s ||
|| 58%, 0 mins elapsed, rate=482.9k bps/s ||
|| 66%, 0 mins elapsed, rate=539.8k bps/s ||
|| 74%, 0 mins elapsed, rate=594.7k bps/s ||
|| 83%, 0 mins elapsed, rate=648.0k bps/s ||
|| 91%, 0 mins elapsed, rate=698.6k bps/s ||
|| 3.0 GB of memory is needed for index building. ||
|| Build the index... ||
|| 8%, 0 mins elapsed, rate=5.9k bps/s ||
|| 16%, 0 mins elapsed, rate=11.7k bps/s ||
|| 24%, 0 mins elapsed, rate=17.5k bps/s ||
|| 33%, 0 mins elapsed, rate=23.2k bps/s ||
|| 41%, 0 mins elapsed, rate=28.9k bps/s ||
|| 49%, 0 mins elapsed, rate=34.5k bps/s ||
|| 58%, 0 mins elapsed, rate=40.0k bps/s ||
|| 66%, 0 mins elapsed, rate=45.5k bps/s ||
|| 74%, 0 mins elapsed, rate=50.9k bps/s ||
|| 83%, 0 mins elapsed, rate=56.4k bps/s ||
|| 91%, 0 mins elapsed, rate=61.7k 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 2.16.1
//================================= 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 (18-Apr-2024 05:16:06, pid=7432) =================\\
|| ||
|| 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, 6.3 mins elapsed, rate=21.8k reads per second ||
|| 83% completed, 6.3 mins elapsed, rate=0.0k reads per second ||
|| 99% completed, 6.3 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 : 6.4 minutes ||
|| ||
\\============================================================================//
Apr 18 05:22:27 Calculating Mappability Exclusion regions from: /tmp/RtmpNH2q4b/refWithMapExcl/Mappability/AlignedReads.bam
Calculating Mappability Exclusions: /private/tmp/RtmpNH2q4b/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 18 05:22:31 Reference generated without non-polyA reference
Apr 18 05:22:31 Reference generated without Mappability reference
Apr 18 05:22:31 Reference generated without Blacklist exclusion
Apr 18 05:22:31 Converting FASTA to local TwoBitFile...done
Apr 18 05:22:32 Connecting to genome TwoBitFile...done
Apr 18 05:22:32 Making local copy of GTF file...done
Apr 18 05:22:32 Reading source GTF file...done
Apr 18 05:22:32 Processing gtf file...
...genes
...transcripts
...CDS
...exons
done
Apr 18 05:22:33 Gene ontology not prepared for this reference
Apr 18 05:22:36 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 18 05:22:41 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 18 05:22:48 Predicting NMD transcripts from genome sequence
...exonic transcripts
...retained introns
|
| | 0%
|
|======================================================================| 100%
done
Apr 18 05:22:51 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 18 05:22:53 Splice Annotations Filtered
Apr 18 05:22:54 Translating Alternate Splice Peptides...done
Apr 18 05:22:54 Splice Annotations finished
Reference build finished
Apr 18 05:22:56 Running SpliceWiz processBAM
Apr 18 05:22:57 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmpNH2q4b/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/RtmpNH2q4b/02H003.bam processed (534 milliseconds)
Apr 18 05:22:57 SpliceWiz processBAM processed RtmpNH2q4b/02H003.bam
Apr 18 05:22:58 Running SpliceWiz processBAM
Apr 18 05:22:59 Using MulticoreParam 1 threads
Reading reference file
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
Processing BAM file /private/tmp/RtmpNH2q4b/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/RtmpNH2q4b/02H003.bam processed (521 milliseconds)
Apr 18 05:22:59 SpliceWiz processBAM processed RtmpNH2q4b/02H003.bam
Apr 18 05:23:00 Reference generated without non-polyA reference
Apr 18 05:23:00 Reference generated without Mappability reference
Apr 18 05:23:00 Reference generated without Blacklist exclusion
Apr 18 05:23:00 Converting FASTA to local TwoBitFile...done
Apr 18 05:23:01 Connecting to genome TwoBitFile...done
Apr 18 05:23:01 Making local copy of GTF file...done
Apr 18 05:23:01 Reading source GTF file...done
Apr 18 05:23:01 Processing gtf file...
...genes
...transcripts
...CDS
Apr 18 05:23:02 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 18 05:23:02 Gene ontology not prepared for this reference
Apr 18 05:23:05 Processing introns...
...data
...basic annotations
...splice motifs
...other info
...defining flanking exon clusters
done
Apr 18 05:23:10 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 18 05:23:18 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 18 05:23:19 Splice Annotations Filtered
Reference build finished
Apr 18 05:23:22 Running SpliceWiz processBAM
Apr 18 05:23:23 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H003.bam processed (526 milliseconds)
Apr 18 05:23:24 SpliceWiz processBAM processed RtmpNH2q4b/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H025.bam processed (428 milliseconds)
Apr 18 05:23:24 SpliceWiz processBAM processed RtmpNH2q4b/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H026.bam processed (652 milliseconds)
Apr 18 05:23:25 SpliceWiz processBAM processed RtmpNH2q4b/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H033.bam processed (658 milliseconds)
Apr 18 05:23:26 SpliceWiz processBAM processed RtmpNH2q4b/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H043.bam processed (416 milliseconds)
Apr 18 05:23:26 SpliceWiz processBAM processed RtmpNH2q4b/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H046.bam processed (617 milliseconds)
Apr 18 05:23:27 SpliceWiz processBAM processed RtmpNH2q4b/02H046.bam
Apr 18 05:23:28 Using MulticoreParam 1 threads
Apr 18 05:23:28 Validating Experiment; checking COV files...
Apr 18 05:23:28 Compiling Sample Stats
Apr 18 05:23:28 Compiling Junction List...merging...done
Apr 18 05:23:30 Compiling Junction Stats...merging...done
Apr 18 05:23:39 Compiling Intron Retention List...done
Apr 18 05:23:41 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 18 05:23:54 Generating NxtSE assays
Apr 18 05:23:55 Using MulticoreParam 1 threads
|
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|============ | 17%
|
|======================= | 33%
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|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Apr 18 05:24:14 Building Final NxtSE Object
Apr 18 05:24:14 ...consolidating assays to H5 file
Apr 18 05:24:16 ...packaging reference
Apr 18 05:24:16 ...synthesising NxtSE
Apr 18 05:24:16 ...determining how overlapping introns should be removed
Apr 18 05:24:20 SpliceWiz (NxtSE) Collation Finished
Apr 18 05:24:20 Loading NxtSE object from file...
Apr 18 05:24:20 ...loading reference (NxtSE)
Apr 18 05:24:20 ...linking assays
Apr 18 05:24:20 ...linking COV files
Apr 18 05:24:20 ...loading rowData
Apr 18 05:24:20 ...removing overlapping introns...
Apr 18 05:24:20 NxtSE loaded
Apr 18 05:24:20 SpliceWiz reference already exists in given directory
Apr 18 05:24:20 Running SpliceWiz processBAM
Apr 18 05:24:22 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H003.bam processed (525 milliseconds)
Apr 18 05:24:22 SpliceWiz processBAM processed RtmpNH2q4b/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H025.bam processed (453 milliseconds)
Apr 18 05:24:23 SpliceWiz processBAM processed RtmpNH2q4b/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H026.bam processed (667 milliseconds)
Apr 18 05:24:24 SpliceWiz processBAM processed RtmpNH2q4b/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H033.bam processed (637 milliseconds)
Apr 18 05:24:24 SpliceWiz processBAM processed RtmpNH2q4b/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H043.bam processed (419 milliseconds)
Apr 18 05:24:25 SpliceWiz processBAM processed RtmpNH2q4b/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H046.bam processed (607 milliseconds)
Apr 18 05:24:25 SpliceWiz processBAM processed RtmpNH2q4b/02H046.bam
Apr 18 05:24:27 Using MulticoreParam 1 threads
Apr 18 05:24:27 Validating Experiment; checking COV files...
Apr 18 05:24:27 Compiling Sample Stats
Apr 18 05:24:27 Compiling Junction List...merging...done
Apr 18 05:24:28 Compiling Junction Stats...merging...done
Apr 18 05:24:38 Compiling Intron Retention List...done
Apr 18 05:24:40 Compiling Tandem Junction List...merging...done
Apr 18 05:24:41 Tidying up splice junctions and intron retentions...
...annotating splice junctions
...looking for novel exons
Apr 18 05:24:45 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 18 05:24:58 Tidying up splice junctions and intron retentions (part 2)...
...grouping splice junctions
...grouping introns
...loading splice events
...compiling rowEvents
done
Apr 18 05:25:08 Generating NxtSE assays
Apr 18 05:25:10 Using MulticoreParam 1 threads
|
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|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Apr 18 05:25:29 Building Final NxtSE Object
Apr 18 05:25:29 ...consolidating assays to H5 file
Apr 18 05:25:31 ...packaging reference
Apr 18 05:25:31 ...synthesising NxtSE
Apr 18 05:25:31 ...determining how overlapping introns should be removed
Apr 18 05:25:35 SpliceWiz (NxtSE) Collation Finished
Apr 18 05:25:35 Loading NxtSE object from file...
Apr 18 05:25:35 ...loading reference (NxtSE)
Apr 18 05:25:35 ...linking assays
Apr 18 05:25:35 ...linking COV files
Apr 18 05:25:35 ...loading rowData
Apr 18 05:25:35 ...removing overlapping introns...
Apr 18 05:25:35 NxtSE loaded
Apr 18 05:25:35 SpliceWiz reference already exists in given directory
Apr 18 05:25:35 Running SpliceWiz processBAM
Apr 18 05:25:37 Using MulticoreParam 1 threads
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H003.bam processed (550 milliseconds)
Apr 18 05:25:37 SpliceWiz processBAM processed RtmpNH2q4b/02H003.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H025.bam processed (539 milliseconds)
Apr 18 05:25:38 SpliceWiz processBAM processed RtmpNH2q4b/02H025.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H026.bam processed (749 milliseconds)
Apr 18 05:25:39 SpliceWiz processBAM processed RtmpNH2q4b/02H026.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H033.bam processed (697 milliseconds)
Apr 18 05:25:39 SpliceWiz processBAM processed RtmpNH2q4b/02H033.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H043.bam processed (441 milliseconds)
Apr 18 05:25:40 SpliceWiz processBAM processed RtmpNH2q4b/02H043.bam
Allocating memory to 1 threads for SpliceWiz (ompBAM)...initialized (0 milliseconds)
/private/tmp/RtmpNH2q4b/02H046.bam processed (640 milliseconds)
Apr 18 05:25:40 SpliceWiz processBAM processed RtmpNH2q4b/02H046.bam
Apr 18 05:25:42 Using MulticoreParam 1 threads
Apr 18 05:25:42 Validating Experiment; checking COV files...
Apr 18 05:25:42 Compiling Sample Stats
Apr 18 05:25:42 Compiling Junction List...merging...done
Apr 18 05:25:43 Compiling Junction Stats...merging...done
Apr 18 05:25:53 Compiling Intron Retention List...done
Apr 18 05:25:55 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 18 05:26:09 Generating NxtSE assays
Apr 18 05:26:10 Using MulticoreParam 1 threads
|
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|
|============ | 17%
|
|======================= | 33%
|
|=================================== | 50%
|
|=============================================== | 67%
|
|========================================================== | 83%
|
|======================================================================| 100%
Apr 18 05:26:30 Building Final NxtSE Object
Apr 18 05:26:30 ...consolidating assays to H5 file
Apr 18 05:26:31 ...packaging reference
Apr 18 05:26:31 ...synthesising NxtSE
Apr 18 05:26:32 ...determining how overlapping introns should be removed
Apr 18 05:26:35 SpliceWiz (NxtSE) Collation Finished
Apr 18 05:26:35 Loading NxtSE object from file...
Apr 18 05:26:35 ...loading reference (NxtSE)
Apr 18 05:26:35 ...linking assays
Apr 18 05:26:35 ...linking COV files
Apr 18 05:26:35 ...loading rowData
Apr 18 05:26:35 ...removing overlapping introns...
Apr 18 05:26:35 NxtSE loaded
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 57 ]
>
> # bump to trigger r cmd check
>
> proc.time()
user system elapsed
416.275 236.277 671.658
SpliceWiz.Rcheck/SpliceWiz-Ex.timings
| name | user | system | elapsed | |
| ASE-GLM-edgeR | 2.637 | 0.079 | 2.725 | |
| ASE-methods | 36.919 | 0.295 | 37.735 | |
| ASEFilter-class | 0.043 | 0.003 | 0.047 | |
| Build-Reference-methods | 84.851 | 1.587 | 90.582 | |
| Coverage | 0.990 | 0.049 | 1.079 | |
| Gene-ontology-methods | 1.828 | 0.083 | 1.998 | |
| Graphics-User-Interface | 0 | 0 | 0 | |
| Mappability-methods | 3.097 | 0.042 | 3.197 | |
| NxtSE-class | 65.834 | 0.917 | 69.109 | |
| Run_SpliceWiz_Filters | 9.316 | 0.044 | 9.565 | |
| STAR-methods | 0.004 | 0.015 | 0.036 | |
| View-Reference-methods | 0.266 | 0.025 | 0.307 | |
| collateData | 3.122 | 0.062 | 3.320 | |
| coord2GR | 0.028 | 0.002 | 0.034 | |
| covDataObject-class | 1.258 | 0.030 | 1.471 | |
| covPlotObject-class | 20.683 | 0.475 | 21.580 | |
| covPlotly-class | 1.041 | 0.025 | 1.069 | |
| example-SpliceWiz-data | 0.019 | 0.002 | 0.022 | |
| findSamples | 0.004 | 0.004 | 0.008 | |
| isCOV | 0.019 | 0.003 | 0.022 | |
| makeSE | 2.042 | 0.077 | 2.125 | |
| make_plot_data | 0.066 | 0.002 | 0.070 | |
| plotCoverage | 13.722 | 0.178 | 14.046 | |
| processBAM | 5.072 | 0.721 | 3.992 | |
| setSWthreads | 0.003 | 0.009 | 0.017 | |
| theme_white | 0.155 | 0.050 | 0.205 | |