Valerie Obenchain
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/VariantAnnotation |
| Branch: RELEASE_3_8 |
| Last Commit: 0393347 |
| Last Changed Date: 2019-03-19 13:28:03 -0400 (Tue, 19 Mar 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:49:16 -0400 (Tue, 16 Apr 2019).
| Package 1617/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| VariantAnnotation 1.28.13 Valerie Obenchain
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ OK ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: VariantAnnotation |
| Version: 1.28.13 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings VariantAnnotation_1.28.13.tar.gz |
| StartedAt: 2019-04-16 03:37:26 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 03:45:19 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 472.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: VariantAnnotation.Rcheck |
| Warnings: 0 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:VariantAnnotation.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings VariantAnnotation_1.28.13.tar.gz
###
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##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/VariantAnnotation.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘VariantAnnotation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘VariantAnnotation’ version ‘1.28.13’
* 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 ‘VariantAnnotation’ 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
'library' or 'require' call to ‘snpStats’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported objects imported by ':::' calls:
‘BiocGenerics:::replaceSlots’ ‘BiocGenerics:::testPackage’
‘Rsamtools:::.RsamtoolsFile’ ‘Rsamtools:::.RsamtoolsFileList’
‘Rsamtools:::.io_check_exists’ ‘S4Vectors:::expandByColumnSet’
‘S4Vectors:::labeledLine’ ‘S4Vectors:::recycleVector’
‘S4Vectors:::selectSome’
‘SummarizedExperiment:::.SummarizedExperiment.charbound’
‘SummarizedExperiment:::.cbind.DataFrame’
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
.predictCodingGRangesList: no visible binding for global variable
‘GENETIC_CODE’
VRangesForMatching: no visible binding for global variable ‘REF’
VRangesForMatching: no visible binding for global variable ‘ALT’
probabilityToSnpMatrix: no visible global function definition for
‘post2g’
import,VcfFile-ANY-ANY: no visible global function definition for
‘checkArgFormat’
Undefined global functions or variables:
ALT GENETIC_CODE REF checkArgFormat post2g
* 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
File ‘/home/biocbuild/bbs-3.8-bioc/R/library/VariantAnnotation/libs/VariantAnnotation.so’:
Found ‘stderr’, possibly from ‘stderr’ (C)
File ‘VariantAnnotation/libs/VariantAnnotation.so’:
Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’
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. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
locateVariants-methods 31.996 0.216 32.251
predictCoding-methods 28.212 0.036 28.323
summarizeVariants-methods 9.264 0.012 9.285
PROVEANDb-class 6.788 0.624 12.416
PolyPhenDb-class 1.004 0.084 5.138
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘VariantAnnotation_unit_tests.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
‘/home/biocbuild/bbs-3.8-bioc/meat/VariantAnnotation.Rcheck/00check.log’
for details.
VariantAnnotation.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL VariantAnnotation ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘VariantAnnotation’ ... ** libs gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c IRanges_stubs.c -o IRanges_stubs.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c R_init_VariantAnnotation.c -o R_init_VariantAnnotation.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c XVector_stubs.c -o XVector_stubs.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c dna_hash.c -o dna_hash.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c rle.c -o rle.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c strhash.c -o strhash.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c utilities.c -o utilities.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c vcffile.c -o vcffile.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c vcftype.c -o vcftype.o gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/include" -I/usr/local/include -fpic -g -O2 -Wall -c writevcf.c -o writevcf.o gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o VariantAnnotation.so Biostrings_stubs.o IRanges_stubs.o R_init_VariantAnnotation.o XVector_stubs.o dna_hash.o rle.o strhash.o utilities.o vcffile.o vcftype.o writevcf.o /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.8-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/library/VariantAnnotation/libs ** R ** inst ** byte-compile and prepare package for lazy loading Creating a new generic function for ‘tabulate’ in package ‘VariantAnnotation’ ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (VariantAnnotation)
VariantAnnotation.Rcheck/tests/VariantAnnotation_unit_tests.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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.
> require("VariantAnnotation") || stop("unable to load VariantAnnotation package")
Loading required package: VariantAnnotation
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, colMeans, colSums, colnames,
dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
intersect, is.unsorted, lapply, lengths, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which, which.max, which.min
Loading required package: GenomeInfoDb
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
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
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
Attaching package: 'VariantAnnotation'
The following object is masked from 'package:base':
tabulate
[1] TRUE
> VariantAnnotation:::.test()
Loading required package: RSQLite
starting prefilter
prefiltering 10376 records
prefiltered to /tmp/RtmphGakuf/file18ed28aa9f68
compressing and indexing '/tmp/RtmphGakuf/file18ed28aa9f68'
starting filter
filtering 10376 records
completed filtering
compressing and indexing '/tmp/RtmphGakuf/file18ed1f06c4d7'
Loading required package: survival
Loading required package: Matrix
Attaching package: 'Matrix'
The following object is masked from 'package:VariantAnnotation':
expand
The following object is masked from 'package:S4Vectors':
expand
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
non-single nucleotide variations are set to NA
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
'select()' returned 1:1 mapping between keys and columns
Loading required package: BSgenome
Loading required package: rtracklayer
'select()' returned many:1 mapping between keys and columns
RUNIT TEST PROTOCOL -- Tue Apr 16 03:45:14 2019
***********************************************
Number of test functions: 97
Number of errors: 0
Number of failures: 0
1 Test Suite :
VariantAnnotation RUnit Tests - 97 test functions, 0 errors, 0 failures
Number of test functions: 97
Number of errors: 0
Number of failures: 0
Warning messages:
1: info fields with no header: noMatch
2: In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
3: In DataFrame(..., check.names = FALSE) : NAs introduced by coercion
4: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 7 out-of-bound ranges located on sequence
70477. Note that ranges located on a sequence whose length is unknown
(NA) or on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
5: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) :
GRanges object contains 6 out-of-bound ranges located on sequence
70477. Note that ranges located on a sequence whose length is unknown
(NA) or on a circular sequence are not considered out-of-bound (use
seqlengths() and isCircular() to get the lengths and circularity flags
of the underlying sequences). You can use trim() to trim these ranges.
See ?`trim,GenomicRanges-method` for more information.
>
> proc.time()
user system elapsed
128.540 1.252 132.003
VariantAnnotation.Rcheck/VariantAnnotation-Ex.timings
| name | user | system | elapsed | |
| GLtoGP | 1.596 | 0.204 | 1.841 | |
| PROVEANDb-class | 6.788 | 0.624 | 12.416 | |
| PolyPhenDb-class | 1.004 | 0.084 | 5.138 | |
| SIFTDb-class | 0.000 | 0.000 | 0.001 | |
| ScanVcfParam-class | 1.284 | 0.036 | 1.352 | |
| VCF-class | 1.884 | 0.000 | 1.888 | |
| VCFHeader-class | 0.120 | 0.000 | 0.122 | |
| VRanges-class | 0.724 | 0.000 | 0.727 | |
| VRangesList-class | 0.48 | 0.00 | 0.49 | |
| VariantType-class | 0.008 | 0.000 | 0.007 | |
| VcfFile-class | 0.860 | 0.000 | 0.886 | |
| filterVcf-methods | 3.132 | 0.036 | 3.185 | |
| genotypeToSnpMatrix-methods | 1.684 | 0.084 | 1.770 | |
| getTranscriptSeqs-methods | 0.000 | 0.000 | 0.001 | |
| indexVcf-method | 0.016 | 0.000 | 0.035 | |
| isSNV-methods | 1.788 | 0.004 | 1.795 | |
| locateVariants-methods | 31.996 | 0.216 | 32.251 | |
| predictCoding-methods | 28.212 | 0.036 | 28.323 | |
| probabilityToSnpMatrix | 0.068 | 0.000 | 0.066 | |
| readVcf-methods | 4.128 | 0.004 | 4.147 | |
| scanVcf-methods | 0.348 | 0.000 | 0.346 | |
| seqinfo-method | 0.104 | 0.000 | 0.103 | |
| snpSummary | 0.476 | 0.004 | 0.483 | |
| summarizeVariants-methods | 9.264 | 0.012 | 9.285 | |
| writeVcf-methods | 1.636 | 0.004 | 1.644 | |