Haakon Tjeldnes
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/ORFik |
| Branch: RELEASE_3_10 |
| Last Commit: 3cc10e4 |
| Last Changed Date: 2020-02-06 03:37:06 -0400 (Thu, 06 Feb 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:47:28 -0400 (Wed, 15 Apr 2020).
| Package 1200/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| ORFik 1.6.9 Haakon Tjeldnes
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: ORFik |
| Version: 1.6.9 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ORFik_1.6.9.tar.gz |
| StartedAt: 2020-04-15 04:23:45 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:32:01 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 495.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ORFik.Rcheck |
| Warnings: 0 |
##############################################################################
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###
### Running command:
###
### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:ORFik.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings ORFik_1.6.9.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/ORFik.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ORFik/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ORFik’ version ‘1.6.9’
* 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 ‘ORFik’ 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 ... NOTE
Unexported objects imported by ':::' calls:
‘GenomicFeatures:::.merge_seqinfo_and_infer_missing_seqlengths’
‘IRanges:::regroupBySupergroup’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ORFikQC: no visible binding for global variable ‘leaders’
ORFikQC: no visible binding for global variable ‘ratio_mrna_aligned’
ORFikQC: no visible binding for global variable ‘mRNA’
ORFikQC: no visible binding for global variable ‘ratio_cds_mrna’
ORFikQC: no visible binding for global variable ‘CDS’
ORFikQC: no visible binding for global variable ‘ratio_cds_leader’
ORFikQC: no visible binding for global variable ‘LEADERS’
ORFikQC: no visible binding for global variable ‘tx’
ORFikQC: no visible global function definition for ‘write.csv’
QCplots: no visible binding for global variable ‘leaders’
QCplots: no visible binding for global variable ‘trailers’
allFeaturesHelper: no visible binding for global variable ‘te’
allFeaturesHelper: no visible binding for global variable ‘fpkmRFP’
allFeaturesHelper: no visible binding for global variable ‘fpkmRNA’
allFeaturesHelper: no visible binding for global variable ‘countRFP’
allFeaturesHelper: no visible binding for global variable ‘entropyRFP’
allFeaturesHelper: no visible binding for global variable
‘disengagementScores’
allFeaturesHelper: no visible binding for global variable ‘RRS’
allFeaturesHelper: no visible binding for global variable ‘RSS’
allFeaturesHelper: no visible binding for global variable
‘fractionLengths’
allFeaturesHelper: no visible binding for global variable ‘ORFScores’
allFeaturesHelper: no visible binding for global variable ‘ioScore’
allFeaturesHelper: no visible binding for global variable ‘kozak’
allFeaturesHelper: no visible binding for global variable ‘distORFCDS’
allFeaturesHelper: no visible binding for global variable ‘inFrameCDS’
allFeaturesHelper: no visible binding for global variable
‘isOverlappingCds’
allFeaturesHelper: no visible binding for global variable ‘rankInTx’
convertToOneBasedRanges: no visible binding for global variable ‘size’
convertToOneBasedRanges: no visible global function definition for ‘.’
coverageHeatMap: no visible binding for global variable ‘position’
coverageHeatMap: no visible binding for global variable ‘fraction’
coveragePerTiling: no visible binding for global variable ‘ones’
coveragePerTiling: no visible binding for global variable ‘position’
coveragePerTiling: no visible binding for global variable ‘frame’
coverageScorings: no visible binding for global variable ‘count’
coverageScorings: no visible binding for global variable ‘zscore’
coverageScorings: no visible binding for global variable ‘windowMean’
coverageScorings: no visible binding for global variable ‘windowSD’
coverageScorings: no visible global function definition for ‘.’
coverageScorings: no visible binding for global variable ‘gene_sum’
create.experiment: no visible global function definition for ‘View’
detectRibosomeShifts: no visible global function definition for ‘.’
detectRibosomeShifts: no visible binding for global variable ‘fraction’
detectRibosomeShifts: no visible binding for global variable
‘offsets_start’
entropy: no visible binding for global variable ‘Hx’
entropy: no visible binding for global variable ‘codonSums’
entropy: no visible global function definition for ‘.’
filterTranscripts: no visible binding for global variable ‘utr5_len’
filterTranscripts: no visible binding for global variable ‘utr3_len’
gSort: no visible binding for global variable ‘grnames’
getNGenesCoverage: no visible global function definition for ‘.’
getNGenesCoverage: no visible binding for global variable ‘fraction’
initiationScore: no visible global function definition for ‘.’
initiationScore: no visible binding for global variable ‘dif’
initiationScore: no visible binding for global variable ‘fraction’
initiationScore: no visible binding for global variable ‘difPer’
kozakHeatmap: no visible global function definition for ‘.’
kozakHeatmap: no visible binding for global variable ‘variable’
kozakHeatmap: no visible binding for global variable ‘value’
kozakHeatmap: no visible binding for global variable
‘count_seq_pos_with_count’
kozakHeatmap: no visible binding for global variable ‘median_score’
longestORFs: no visible global function definition for ‘.’
metaWindow: no visible binding for global variable ‘position’
metaWindow: no visible binding for global variable ‘frame’
orfScore: no visible binding for global variable ‘frame’
orfScore: no visible binding for global variable ‘frame_one_RP’
orfScore: no visible binding for global variable ‘frame_two_RP’
pSitePlot: no visible binding for global variable ‘count’
pSitePlot: no visible binding for global variable ‘frame’
pSitePlot: no visible binding for global variable ‘position’
read.experiment: no visible global function definition for ‘read.table’
read.experiment: no visible global function definition for ‘read.csv2’
remakeTxdbExonIds: no visible global function definition for ‘.’
remakeTxdbExonIds: no visible binding for global variable ‘chr’
removeTxdbExons: no visible binding for global variable ‘exon_rank’
removeTxdbExons: no visible binding for global variable ‘ranks’
rnaNormalize: no visible binding for global variable ‘feature’
save.experiment: no visible global function definition for
‘write.table’
scaledWindowPositions: no visible binding for global variable
‘scalingFactor’
scaledWindowPositions: no visible binding for global variable
‘position’
scaledWindowPositions: no visible global function definition for ‘.’
scoreSummarizedExperiment: no visible global function definition for
‘rowSums2’
transcriptWindow: no visible binding for global variable ‘fractions’
windowCoveragePlot: no visible binding for global variable ‘feature’
windowCoveragePlot: no visible binding for global variable ‘fraction’
windowCoveragePlot: no visible binding for global variable
‘fraction_min’
windowCoveragePlot: no visible binding for global variable ‘position’
nrow,experiment: no visible global function definition for ‘as’
show,experiment: no visible global function definition for ‘as’
Undefined global functions or variables:
. CDS Hx LEADERS ORFScores RRS RSS View as chr codonSums count
countRFP count_seq_pos_with_count dif difPer disengagementScores
distORFCDS entropyRFP exon_rank feature fpkmRFP fpkmRNA fraction
fractionLengths fraction_min fractions frame frame_one_RP
frame_two_RP gene_sum grnames inFrameCDS ioScore isOverlappingCds
kozak leaders mRNA median_score offsets_start ones position rankInTx
ranks ratio_cds_leader ratio_cds_mrna ratio_mrna_aligned read.csv2
read.table rowSums2 scalingFactor size te trailers tx utr3_len
utr5_len value variable windowMean windowSD write.csv write.table
zscore
Consider adding
importFrom("graphics", "frame")
importFrom("methods", "as")
importFrom("utils", "View", "read.csv2", "read.table", "write.csv",
"write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 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 compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
computeFeatures 13.686 4.752 9.881
entropy 4.076 2.532 1.506
findMapORFs 2.595 3.334 1.066
orfScore 2.758 2.497 1.153
* 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: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.10-bioc/meat/ORFik.Rcheck/00check.log’
for details.
ORFik.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL ORFik ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘ORFik’ ... ** using staged installation ** libs clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c RcppExports.cpp -o RcppExports.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c findORFsHelpers.cpp -o findORFsHelpers.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfs.cpp -o findOrfs.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c findOrfsFasta.cpp -o findOrfsFasta.o clang++ -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rcpp/include" -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include -fPIC -Wall -g -O2 -c pmapFromTranscripts.cpp -o pmapFromTranscripts.o clang++ -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 ORFik.so RcppExports.o findORFsHelpers.o findOrfs.o findOrfsFasta.o pmapFromTranscripts.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation installing to /Library/Frameworks/R.framework/Versions/3.6/Resources/library/00LOCK-ORFik/00new/ORFik/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 (ORFik)
ORFik.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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(ORFik)
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicAlignments
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: DelayedArray
Loading required package: matrixStats
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Loading required package: BiocParallel
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
Loading required package: Rsamtools
>
> test_check("ORFik")
Error in x$.self$finalize() : attempt to apply non-function
Error in (function (x) : attempt to apply non-function
[1] "ORFik_cage"
[1] "ORFik_ribo-seq_fheart"
[1] "ORFik_ribo-seq"
[1] "ORFik_rna-seq"
[1] "ORFik_ribo-seq"
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 293 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
146.582 62.057 97.693
ORFik.Rcheck/ORFik-Ex.timings
| name | user | system | elapsed | |
| ORFikQC | 0.462 | 0.005 | 0.468 | |
| assignTSSByCage | 0 | 0 | 0 | |
| computeFeatures | 13.686 | 4.752 | 9.881 | |
| computeFeaturesCage | 0.000 | 0.000 | 0.001 | |
| countTable | 0.328 | 0.001 | 0.332 | |
| coverageHeatMap | 2.410 | 1.472 | 1.553 | |
| coveragePerTiling | 0.486 | 0.001 | 0.498 | |
| coverageScorings | 0.034 | 0.021 | 0.016 | |
| create.experiment | 0.760 | 0.565 | 0.358 | |
| defineTrailer | 0.236 | 0.001 | 0.241 | |
| detectRibosomeShifts | 0.000 | 0.001 | 0.000 | |
| disengagementScore | 0.771 | 0.002 | 0.781 | |
| distToCds | 0.404 | 0.001 | 0.408 | |
| distToTSS | 0.419 | 0.001 | 0.427 | |
| entropy | 4.076 | 2.532 | 1.506 | |
| experiment-class | 0.002 | 0.003 | 0.001 | |
| extendLeaders | 2.106 | 1.850 | 1.050 | |
| extendTrailers | 1.838 | 1.768 | 0.925 | |
| filterTranscripts | 2.321 | 1.044 | 1.735 | |
| fimport | 0.246 | 0.014 | 0.263 | |
| findMapORFs | 2.595 | 3.334 | 1.066 | |
| findORFs | 0.402 | 0.638 | 0.135 | |
| findORFsFasta | 0.278 | 0.461 | 0.088 | |
| findUORFs | 0.002 | 0.003 | 0.001 | |
| firstEndPerGroup | 0.359 | 0.591 | 0.115 | |
| firstExonPerGroup | 0.149 | 0.106 | 0.096 | |
| firstStartPerGroup | 0.084 | 0.001 | 0.086 | |
| floss | 0.239 | 0.001 | 0.247 | |
| fpkm | 0.066 | 0.000 | 0.067 | |
| fractionLength | 0.094 | 0.000 | 0.095 | |
| fread.bed | 0.034 | 0.006 | 0.040 | |
| gcContent | 1.620 | 2.027 | 0.791 | |
| groupGRangesBy | 0.067 | 0.000 | 0.068 | |
| groupings | 0.065 | 0.001 | 0.069 | |
| initiationScore | 2.662 | 0.707 | 1.600 | |
| insideOutsideORF | 2.429 | 2.015 | 1.603 | |
| isInFrame | 0.356 | 0.003 | 0.369 | |
| isOverlapping | 0.320 | 0.001 | 0.328 | |
| kozakHeatmap | 0.000 | 0.000 | 0.001 | |
| kozakSequenceScore | 1.414 | 1.000 | 0.978 | |
| lastExonEndPerGroup | 0.101 | 0.000 | 0.104 | |
| lastExonPerGroup | 0.118 | 0.001 | 0.121 | |
| lastExonStartPerGroup | 0.095 | 0.000 | 0.096 | |
| loadRegion | 0.912 | 0.003 | 0.923 | |
| loadRegions | 1.192 | 0.019 | 1.222 | |
| loadTxdb | 0.136 | 0.003 | 0.140 | |
| longestORFs | 0.672 | 0.005 | 0.254 | |
| makeORFNames | 0.490 | 0.718 | 0.161 | |
| makeSummarizedExperimentFromBam | 0.312 | 0.012 | 0.327 | |
| metaWindow | 0.302 | 0.046 | 0.316 | |
| numExonsPerGroup | 0.252 | 0.383 | 0.082 | |
| orfScore | 2.758 | 2.497 | 1.153 | |
| outputLibs | 2.149 | 0.138 | 0.381 | |
| overlapsToCoverage | 0.088 | 0.000 | 0.089 | |
| pSitePlot | 0.601 | 0.003 | 0.618 | |
| pmapFromTranscriptF | 0.159 | 0.001 | 0.161 | |
| rankOrder | 0.122 | 0.001 | 0.124 | |
| read.experiment | 0.302 | 0.001 | 0.306 | |
| readBam | 0.129 | 0.007 | 0.138 | |
| readWidths | 0.017 | 0.000 | 0.018 | |
| reassignTSSbyCage | 1.470 | 0.604 | 0.946 | |
| reassignTxDbByCage | 0.001 | 0.000 | 0.001 | |
| reduceKeepAttr | 0.851 | 0.575 | 0.434 | |
| remove.experiments | 0.313 | 0.001 | 0.320 | |
| ribosomeReleaseScore | 0.283 | 0.001 | 0.296 | |
| ribosomeStallingScore | 0.523 | 0.001 | 0.527 | |
| save.experiment | 0.335 | 0.001 | 0.339 | |
| scaledWindowPositions | 1.057 | 0.639 | 0.641 | |
| seqnamesPerGroup | 0.402 | 0.373 | 0.130 | |
| shiftFootprints | 0.002 | 0.002 | 0.001 | |
| sortPerGroup | 1.450 | 1.042 | 0.554 | |
| startCodons | 1.850 | 0.771 | 1.031 | |
| startDefinition | 0.001 | 0.000 | 0.001 | |
| startSites | 1.349 | 0.809 | 0.639 | |
| stopCodons | 1.874 | 1.091 | 1.068 | |
| stopDefinition | 0.001 | 0.001 | 0.001 | |
| stopSites | 1.761 | 0.917 | 0.677 | |
| strandBool | 0.009 | 0.001 | 0.011 | |
| strandPerGroup | 0.124 | 0.001 | 0.128 | |
| tile1 | 0.402 | 0.002 | 0.414 | |
| transcriptWindow | 1.532 | 0.003 | 1.559 | |
| translationalEff | 0.181 | 0.000 | 0.188 | |
| txNames | 0.081 | 0.000 | 0.081 | |
| uORFSearchSpace | 1.456 | 0.442 | 1.083 | |
| uniqueGroups | 0.255 | 0.001 | 0.260 | |
| uniqueOrder | 0.715 | 0.304 | 0.462 | |
| unlistGrl | 0.202 | 0.140 | 0.069 | |
| widthPerGroup | 0.248 | 0.185 | 0.087 | |
| windowCoveragePlot | 1.982 | 0.883 | 1.194 | |
| windowPerGroup | 0.523 | 0.001 | 0.528 | |